6NMS

Blocking Fab 136 anti-SIRP-alpha antibody in complex with SIRP-alpha Variant 1

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A [auth L]	d6nmsl1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A [auth L]	d6nmsl2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth A]	d6nmsa1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D [auth A]	d6nmsa2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth H]	d6nmsh_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth B]	d6nmsb_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth S]	d6nmss_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F [auth C]	d6nmsc_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth L]	C1-set_4	e6nmsL2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
A [auth L]	V-set	e6nmsL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
D [auth A]	C1-set_4	e6nmsA2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
D [auth A]	V-set	e6nmsA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)
B [auth H]	C1-set_1	e6nmsH2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
B [auth H]	V-set_10	e6nmsH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_10	ECOD (1.6)
E [auth B]	C1-set_1	e6nmsB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
E [auth B]	V-set_10	e6nmsB2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_10	ECOD (1.6)
C [auth S]	V-set_6	e6nmsS1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_6	ECOD (1.6)
F [auth C]	V-set_6	e6nmsC1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_6	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
D [auth A]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
B [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
E [auth B]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
C [auth S]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)
F [auth C]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (utative)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
A [auth L], D [auth A]	Fab 136, anti-SIRP-alpha	L-KAPPA	Homo sapiens (human)	IGKV3-2001, IGKJ401, IGKJ402, IGKC01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202415-0)
B [auth H], E [auth B]	Fab 136, anti-SIRP-alpha	VH-CH1	Homo sapiens (human)	IGHV3-2304, IGHJ401, IGHJ501, IGHJ502, IGHJ402, IGHJ403, IGHG101, IGHG102, IGHG104, IGHG105, IGHG112, IGHG114, IGHG113, IGHG109, IGHG110, IGHG107, IGHG1*11	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202415-0)
C [auth S], F [auth C]	SIRPA, Tyrosine-protein phosphatase non-receptor type substrate 1	1V-LIKE	Homo sapiens (human)	SIRPA	V-LIKE-DOMAIN V-LIKE	RPI	1V-LIKE	IMGT (202415-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A [auth L], D [auth A]	Light Chain	IGKV3	Kappa	tyrosine-protein phosphatase non-receptor type substrate 1	SAbDab (2024-04-19)
B [auth H], E [auth B]	Heavy Chain	IGHV3	-	tyrosine-protein phosphatase non-receptor type substrate 1	SAbDab (2024-04-19)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth S], F [auth C]	PF07686	Immunoglobulin V-set domain (V-set)	Immunoglobulin V-set domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth L], D [auth A]	Fab 136 anti-SIRP-alpha antibody Variable Light Chain	-	-	-
B [auth H], E [auth B]	Fab 136 anti-SIRP-alpha antibody Variable Heavy Chain	-	-	-
C [auth S], F [auth C]	Tyrosine-protein phosphatase non-receptor type substrate 1	protein antigen binding protein binding binding antigen binding protein phosphatase binding phosphatase binding enzyme binding SH3 domain binding protein domain specific binding cell adhesion molecule binding cell adhesion mediator activity cell-cell adhesion mediator activity GTPase regulator activity enzyme regulator activity protein antigen binding protein binding binding antigen binding protein phosphatase binding phosphatase binding enzyme binding SH3 domain binding protein domain specific binding cell adhesion molecule binding cell adhesion mediator activity cell-cell adhesion mediator activity GTPase regulator activity enzyme regulator activity nucleoside-triphosphatase regulator activity molecular function regulator activity protein binding involved in heterotypic cell-cell adhesion protein tyrosine kinase binding kinase binding protein kinase binding	multicellular organismal process regulation of tumor necrosis factor production regulation of cellular process cellular biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process negative regulation of tumor necrosis factor production organic substance metabolic process cytokine production organic substance biosynthetic process regulation of cytokine production negative regulation of cellular process regulation of multicellular organismal process negative regulation of macromolecule metabolic process multicellular organismal process regulation of tumor necrosis factor production regulation of cellular process cellular biosynthetic process negative regulation of biological process negative regulation of cellular metabolic process negative regulation of tumor necrosis factor production organic substance metabolic process cytokine production organic substance biosynthetic process regulation of cytokine production negative regulation of cellular process regulation of multicellular organismal process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process cellular metabolic process negative regulation of metabolic process biological regulation tumor necrosis factor superfamily cytokine production regulation of cellular metabolic process negative regulation of cytokine production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process tumor necrosis factor production negative regulation of cellular biosynthetic process regulation of cellular biosynthetic process regulation of gene expression negative regulation of gene expression regulation of tumor necrosis factor superfamily cytokine production biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of tumor necrosis factor superfamily cytokine production metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process negative regulation of multicellular organismal process regulation of metabolic process interleukin-6 production regulation of interleukin-6 production negative regulation of interleukin-6 production leukocyte migration immune system process mononuclear cell migration cellular extravasation myeloid leukocyte migration cell migration cell motility monocyte extravasation regulation of protein modification process regulation of protein phosphorylation negative regulation of phosphate metabolic process regulation of primary metabolic process regulation of phosphate metabolic process phosphate-containing compound metabolic process negative regulation of protein modification process protein metabolic process protein modification process phosphorus metabolic process negative regulation of protein metabolic process organonitrogen compound metabolic process protein phosphorylation phosphorylation regulation of protein metabolic process primary metabolic process negative regulation of protein phosphorylation macromolecule modification negative regulation of phosphorus metabolic process regulation of phosphorylation regulation of phosphorus metabolic process negative regulation of phosphorylation regulation of defense response response to stimulus regulation of response to external stimulus negative regulation of inflammatory response defense response negative regulation of response to stimulus response to external stimulus regulation of inflammatory response regulation of response to stimulus response to stress negative regulation of response to external stimulus regulation of response to stress negative regulation of defense response inflammatory response regulation of type II interferon production type II interferon production cellular response to stimulus response to organic substance biological process involved in interspecies interaction between organisms response to lipid response to other organism cellular response to lipopolysaccharide response to oxygen-containing compound cellular response to molecule of bacterial origin response to lipopolysaccharide cellular response to oxygen-containing compound response to biotic stimulus cellular response to biotic stimulus cellular response to chemical stimulus response to chemical response to bacterium cellular response to lipid cellular response to organic substance response to external biotic stimulus response to molecule of bacterial origin signaling negative regulation of signaling negative regulation of intracellular signal transduction regulation of signal transduction intracellular signal transduction negative regulation of cell communication cell communication regulation of intracellular signal transduction intracellular signaling cassette signal transduction regulation of signaling regulation of MAPK cascade negative regulation of signal transduction negative regulation of ERK1 and ERK2 cascade MAPK cascade regulation of cell communication ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade negative regulation of MAPK cascade regulation of localization import into cell positive regulation of cellular component organization regulation of cellular component organization transport positive regulation of biological process vesicle-mediated transport cellular component organization localization positive regulation of endocytosis phagocytosis cellular component organization or biogenesis positive regulation of cellular process regulation of endocytosis regulation of transport regulation of phagocytosis regulation of vesicle-mediated transport establishment of localization positive regulation of phagocytosis positive regulation of transport endocytosis regulation of nitric oxide biosynthetic process negative regulation of nitric oxide metabolic process reactive nitrogen species metabolic process nitric oxide metabolic process nitric oxide biosynthetic process negative regulation of nitric oxide biosynthetic process regulation of nitric oxide metabolic process negative regulation of type I interferon production regulation of interferon-beta production interferon-beta production type I interferon production negative regulation of interferon-beta production regulation of type I interferon production negative regulation of JNK cascade JNK cascade regulation of JNK cascade cellular response to oxidative stress cellular response to chemical stress cellular response to hydrogen peroxide response to reactive oxygen species response to inorganic substance response to hydrogen peroxide response to oxidative stress cellular response to reactive oxygen species cellular response to stress chemokine (C-C motif) ligand 5 production negative regulation of chemokine production negative regulation of chemokine (C-C motif) ligand 5 production regulation of chemokine production chemokine production regulation of chemokine (C-C motif) ligand 5 production response to type II interferon response to cytokine cellular response to type II interferon innate immune response cellular response to cytokine stimulus immune response defense response to symbiont defense response to other organism cell adhesion negative regulation of transport negative regulation of endocytosis negative regulation of phagocytosis negative regulation of cellular component organization I-kappaB phosphorylation canonical NF-kappaB signal transduction negative regulation of I-kappaB phosphorylation regulation of I-kappaB phosphorylation interleukin-1 production regulation of interleukin-1 beta production regulation of interleukin-1 production interleukin-1 beta production cellular response to interleukin-12 response to interleukin-12 cellular response to interleukin-1 response to interleukin-1 regulation of leukocyte activation regulation of cell activation positive regulation of leukocyte cell-cell adhesion lymphocyte activation leukocyte cell-cell adhesion leukocyte activation positive regulation of cell-cell adhesion positive regulation of lymphocyte activation positive regulation of cell activation cell-cell adhesion T cell activation positive regulation of leukocyte activation regulation of immune system process regulation of cell-cell adhesion positive regulation of immune system process positive regulation of T cell activation positive regulation of cell adhesion regulation of cell adhesion cell activation regulation of T cell activation regulation of leukocyte cell-cell adhesion positive regulation of multicellular organismal process regulation of lymphocyte activation negative regulation of macrophage inflammatory protein 1 alpha production macrophage inflammatory protein-1 alpha production regulation of macrophage inflammatory protein 1 alpha production regulation of cytokine production involved in inflammatory response negative regulation of cytokine production involved in inflammatory response production of molecular mediator involved in inflammatory response cytokine production involved in inflammatory response	membrane-bounded organelle intracellular anatomical structure tertiary granule membrane membrane intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle endomembrane system tertiary granule intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane cytoplasmic vesicle membrane-bounded organelle intracellular anatomical structure tertiary granule membrane membrane intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle endomembrane system tertiary granule intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane cytoplasmic vesicle organelle secretory granule secretory vesicle cytoplasm vesicle organelle membrane secretory granule membrane extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle cell surface cell periphery plasma membrane ficolin-1-rich granule membrane ficolin-1-rich granule

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth S], F [auth C]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
C [auth S], F [auth C]	IPR003599	Immunoglobulin subtype	Domain
C [auth S], F [auth C]	IPR003597	Immunoglobulin C1-set	Domain
C [auth S], F [auth C]	IPR013106	Immunoglobulin V-set domain	Domain
C [auth S], F [auth C]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
C [auth S], F [auth C]	IPR007110	Immunoglobulin-like domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C [auth S], F [auth C]	Pharos: P78324	primitive neuroectodermal tumor ulcerative colitis atypical teratoid rhabdoid tumor Condition, Preneoplastic interstitial cystitis lung adenocarcinoma malignant glioma non-small cell lung carcinoma precancerous condition psoriasis breast cancer gastric carcinoma invasive ductal breast carcinoma lung cancer malignant mesothelioma primitive neuroectodermal tumor ulcerative colitis atypical teratoid rhabdoid tumor Condition, Preneoplastic interstitial cystitis lung adenocarcinoma malignant glioma non-small cell lung carcinoma precancerous condition psoriasis breast cancer gastric carcinoma invasive ductal breast carcinoma lung cancer malignant mesothelioma osteosarcoma subependymal giant cell astrocytoma breast carcinoma glioblastoma large cell medulloblastoma lung carcinoma medulloblastoma ovarian cancer

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.