3HI6

Crystal structure of intermediate affinity I domain of integrin LFA-1 with the Fab fragment of its antibody AL-57

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 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)
D [auth L]	d3hi6l2	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 L]	d3hi6l1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F [auth Y]	d3hi6y2	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)
F [auth Y]	d3hi6y1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3hi6b_	Alpha and beta proteins (a/b)	vWA-like	vWA-like	Integrin A (or I) domain	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3hi6a_	Alpha and beta proteins (a/b)	vWA-like	vWA-like	Integrin A (or I) domain	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth X]	d3hi6x_	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 H]	d3hi6h_	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)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	vWA-like	8042676	3000832	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	vWA-like	8042676	3000832	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D [auth L]	C1-set_4	e3hi6L2	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 L]	V-set	e3hi6L1	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)
F [auth Y]	C1-set_4	e3hi6Y2	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)
F [auth Y]	V-set	e3hi6Y1	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	VWA	e3hi6B1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: vWA-like	F: VWA	ECOD (1.6)
A	VWA	e3hi6A1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: vWA-like	F: VWA	ECOD (1.6)
E [auth X]	V-set_8	e3hi6X1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
E [auth X]	C1-set_1	e3hi6X2	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)
C [auth H]	V-set_8	e3hi6H1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
C [auth H]	C1-set_1	e3hi6H2	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F [auth Y]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B	3.40.50.410	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	von Willebrand factor, type A domain	CATH (4.3.0)
A	3.40.50.410	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	von Willebrand factor, type A domain	CATH (4.3.0)
E [auth X]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

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
D [auth L], F [auth Y]	Fab AL-57	L-KAPPA	Homo sapiens (human)	IGKV1-3901, IGKV1D-3901, IGKJ101, IGKJ203, IGKJ204, IGKC01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-4_KAPPA	IMGT (202415-0)
A, B	Integrin alpha-L (LFA-1A), L186>C, F324>C	INTEGRIN-ALPHA-L	Homo sapiens (human)	ALPHA-L	I-LIKE-DOMAIN I-DOMAIN	RPI	(INTEGRIN-ALPHA-L)	IMGT (202415-0)
C [auth H], E [auth X]	Fab AL-57	VH-CH1	Homo sapiens (human)	IGHV3-2301, IGHJ302, IGHG401, IGHG404	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-4_KAPPA	IMGT (202415-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
D [auth L], F [auth Y]	Light Chain	IGKV1	Kappa	integrin alpha-l	SAbDab (2024-04-19)
C [auth H], E [auth X]	Heavy Chain	IGHV3	-	integrin alpha-l	SAbDab (2024-04-19)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00092	von Willebrand factor type A domain (VWA)	von Willebrand factor type A domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D [auth L], F [auth Y]	light chain of Fab fragment of AL-57 against alpha L I domain	-	-	-
A, B	Integrin alpha-L	cell adhesion molecule binding protein binding binding ICAM-3 receptor activity molecular transducer activity transmembrane signaling receptor activity signaling receptor activity protein-containing complex binding integrin binding signaling receptor binding cation binding ion binding metal ion binding small molecule binding	cell adhesion cell-matrix adhesion cell-substrate adhesion cellular process T cell extravasation lymphocyte migration memory T cell extravasation leukocyte migration immune system process mononuclear cell migration cellular extravasation cell migration cell motility T cell migration cell adhesion cell-matrix adhesion cell-substrate adhesion cellular process T cell extravasation lymphocyte migration memory T cell extravasation leukocyte migration immune system process mononuclear cell migration cellular extravasation cell migration cell motility T cell migration localization import into cell transport phagocytosis endocytosis establishment of localization vesicle-mediated transport cellular response to stimulus regulation of biological process integrin-mediated signaling pathway regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling biological regulation cell communication signal transduction heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules cell-cell adhesion cell-cell adhesion via plasma-membrane adhesion molecules cell adhesion mediated by integrin leukocyte cell-cell adhesion defense response response to stress inflammatory response protein localization cellular localization receptor clustering cellular macromolecule localization macromolecule localization localization within membrane protein localization to membrane multicellular organismal process immune response cell activation lymphocyte activation cell activation involved in immune response leukocyte activation immune effector process T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell T cell activation involved in immune response T cell activation leukocyte activation involved in immune response lymphocyte activation involved in immune response	membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle endomembrane system specific granule membrane intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane cytoplasmic vesicle organelle membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle endomembrane system specific granule membrane 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 specific granule cell periphery cell surface plasma membrane external side of plasma membrane side of membrane extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle protein-containing complex plasma membrane protein complex membrane protein complex receptor complex integrin complex plasma membrane signaling receptor complex protein complex involved in cell adhesion integrin alphaL-beta2 complex
C [auth H], E [auth X]	Heavy chain of Fab fragment of AL-57 against alpha L I domain	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR013517	FG-GAP repeat	Repeat
A, B	IPR013519	Integrin alpha beta-propellor	Repeat
A, B	IPR000413	Integrin alpha chain	Family
A, B	IPR036465	von Willebrand factor A-like domain superfamily	Homologous Superfamily
A, B	IPR013649	Integrin alpha, first immunoglubulin-like domain	Domain
A, B	IPR028994	Integrin alpha, N-terminal	Homologous Superfamily
A, B	IPR002035	von Willebrand factor, type A	Domain
A, B	IPR048285	Integrin alpha, second immunoglobulin-like domain	Domain
A, B	IPR032695	Integrin domain superfamily	Homologous Superfamily
A, B	IPR018184	Integrin alpha chain, C-terminal cytoplasmic region, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P20701	ulcerative colitis acute promyelocytic leukemia Liver Cirrhosis, Experimental Behcet disease inflammatory bowel disease Sjogren syndrome chronic obstructive pulmonary disease dry eye syndrome interstitial cystitis lung carcinoma osteosarcoma spina bifida atopic eczema glioblastoma malignant glioma ulcerative colitis acute promyelocytic leukemia Liver Cirrhosis, Experimental Behcet disease inflammatory bowel disease Sjogren syndrome chronic obstructive pulmonary disease dry eye syndrome interstitial cystitis lung carcinoma osteosarcoma spina bifida atopic eczema glioblastoma malignant glioma periodontitis psoriasis tuberculosis cutaneous lupus erythematosus lung cancer non-small cell lung carcinoma pilocytic astrocytoma

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.