3CFK

Crystal structure of catalytic elimination antibody 34E4, triclinic crystal form


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

ChainsDomain InfoClassFoldSuperfamilyFamilyDomainSpeciesProvenance Source (Version)
C [auth A]d3cfka1 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin V set domains (antibody variable domain-like) Immunoglobulin light chain kappa variable domain, VL-kappa mouse (Mus musculus ) [TaxId: 10090 ], Human (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
C [auth A]d3cfka2 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin C1 set domains (antibody constant domain-like) Immunoglobulin light chain kappa constant domain, CL-kappa mouse (Mus musculus ) [TaxId: 10090 ], Human (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
E [auth C]d3cfkc1 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin V set domains (antibody variable domain-like) Immunoglobulin light chain kappa variable domain, VL-kappa mouse (Mus musculus ) [TaxId: 10090 ], Human (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
E [auth C]d3cfkc2 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin C1 set domains (antibody constant domain-like) Immunoglobulin light chain kappa constant domain, CL-kappa mouse (Mus musculus ) [TaxId: 10090 ], Human (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
G [auth E]d3cfke1 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin V set domains (antibody variable domain-like) Immunoglobulin light chain kappa variable domain, VL-kappa mouse (Mus musculus ) [TaxId: 10090 ], Human (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
G [auth E]d3cfke2 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin C1 set domains (antibody constant domain-like) Immunoglobulin light chain kappa constant domain, CL-kappa mouse (Mus musculus ) [TaxId: 10090 ], Human (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
K [auth J]d3cfkj1 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin V set domains (antibody variable domain-like) Immunoglobulin light chain kappa variable domain, VL-kappa mouse (Mus musculus ) [TaxId: 10090 ], Human (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
K [auth J]d3cfkj2 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin C1 set domains (antibody constant domain-like) Immunoglobulin light chain kappa constant domain, CL-kappa mouse (Mus musculus ) [TaxId: 10090 ], Human (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
Md3cfkm1 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin V set domains (antibody variable domain-like) Immunoglobulin light chain kappa variable domain, VL-kappa mouse (Mus musculus ) [TaxId: 10090 ], Human (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
Md3cfkm2 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin C1 set domains (antibody constant domain-like) Immunoglobulin light chain kappa constant domain, CL-kappa mouse (Mus musculus ) [TaxId: 10090 ], Human (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
Od3cfko1 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin V set domains (antibody variable domain-like) Immunoglobulin light chain kappa variable domain, VL-kappa mouse (Mus musculus ) [TaxId: 10090 ], Human (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
Od3cfko2 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin C1 set domains (antibody constant domain-like) Immunoglobulin light chain kappa constant domain, CL-kappa mouse (Mus musculus ) [TaxId: 10090 ], Human (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
A [auth L]d3cfkl1 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin V set domains (antibody variable domain-like) Immunoglobulin light chain kappa variable domain, VL-kappa mouse (Mus musculus ) [TaxId: 10090 ], Human (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
A [auth L]d3cfkl2 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin C1 set domains (antibody constant domain-like) Immunoglobulin light chain kappa constant domain, CL-kappa mouse (Mus musculus ) [TaxId: 10090 ], Human (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
I [auth G]d3cfkg1 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin V set domains (antibody variable domain-like) Immunoglobulin light chain kappa variable domain, VL-kappa mouse (Mus musculus ) [TaxId: 10090 ], Human (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
I [auth G]d3cfkg2 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin C1 set domains (antibody constant domain-like) Immunoglobulin light chain kappa constant domain, CL-kappa mouse (Mus musculus ) [TaxId: 10090 ], Human (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
B [auth H]d3cfkh1 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin V set domains (antibody variable domain-like) Immunoglobulin heavy chain variable domain, VH mouse (Mus musculus ) [TaxId: 10090 ], Human (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
B [auth H]d3cfkh2 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin C1 set domains (antibody constant domain-like) Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma mouse (Mus musculus ) [TaxId: 10090 ], Human (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
D [auth B]d3cfkb1 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin V set domains (antibody variable domain-like) Immunoglobulin heavy chain variable domain, VH mouse (Mus musculus ) [TaxId: 10090 ], Human (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
D [auth B]d3cfkb2 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin C1 set domains (antibody constant domain-like) Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma mouse (Mus musculus ) [TaxId: 10090 ], Human (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
F [auth D]d3cfkd1 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin V set domains (antibody variable domain-like) Immunoglobulin heavy chain variable domain, VH mouse (Mus musculus ) [TaxId: 10090 ], Human (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
F [auth D]d3cfkd2 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin C1 set domains (antibody constant domain-like) Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma mouse (Mus musculus ) [TaxId: 10090 ], Human (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
H [auth F]d3cfkf1 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin V set domains (antibody variable domain-like) Immunoglobulin heavy chain variable domain, VH mouse (Mus musculus ) [TaxId: 10090 ], Human (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
H [auth F]d3cfkf2 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin C1 set domains (antibody constant domain-like) Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma mouse (Mus musculus ) [TaxId: 10090 ], Human (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
J [auth I]d3cfki1 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin V set domains (antibody variable domain-like) Immunoglobulin heavy chain variable domain, VH mouse (Mus musculus ) [TaxId: 10090 ], Human (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
J [auth I]d3cfki2 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin C1 set domains (antibody constant domain-like) Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma mouse (Mus musculus ) [TaxId: 10090 ], Human (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
L [auth K]d3cfkk1 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin V set domains (antibody variable domain-like) Immunoglobulin heavy chain variable domain, VH mouse (Mus musculus ) [TaxId: 10090 ], Human (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
L [auth K]d3cfkk2 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin C1 set domains (antibody constant domain-like) Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma mouse (Mus musculus ) [TaxId: 10090 ], Human (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
Nd3cfkn1 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin V set domains (antibody variable domain-like) Immunoglobulin heavy chain variable domain, VH mouse (Mus musculus ) [TaxId: 10090 ], Human (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
Nd3cfkn2 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin C1 set domains (antibody constant domain-like) Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma mouse (Mus musculus ) [TaxId: 10090 ], Human (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
Pd3cfkp1 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin V set domains (antibody variable domain-like) Immunoglobulin heavy chain variable domain, VH mouse (Mus musculus ) [TaxId: 10090 ], Human (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)
Pd3cfkp2 All beta proteins Immunoglobulin-like beta-sandwich Immunoglobulin C1 set domains (antibody constant domain-like) Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma mouse (Mus musculus ) [TaxId: 10090 ], Human (Homo sapiens ) [TaxId: 9606 ], SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
C [auth A]PF07654e3cfkA2 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07654ECOD (1.6)
C [auth A]PF07686e3cfkA1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07686ECOD (1.6)
E [auth C]PF07654e3cfkC2 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07654ECOD (1.6)
E [auth C]PF07686e3cfkC1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07686ECOD (1.6)
G [auth E]PF07654e3cfkE2 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07654ECOD (1.6)
G [auth E]PF07686e3cfkE1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07686ECOD (1.6)
K [auth J]PF07654e3cfkJ2 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07654ECOD (1.6)
K [auth J]PF07686e3cfkJ1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07686ECOD (1.6)
MPF07654e3cfkM2 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07654ECOD (1.6)
MPF07686e3cfkM1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07686ECOD (1.6)
OPF07654e3cfkO2 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07654ECOD (1.6)
OPF07686e3cfkO1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07686ECOD (1.6)
A [auth L]PF07654e3cfkL2 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07654ECOD (1.6)
A [auth L]PF07686e3cfkL1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07686ECOD (1.6)
I [auth G]PF07654e3cfkG2 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07654ECOD (1.6)
I [auth G]PF07686e3cfkG1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07686ECOD (1.6)
B [auth H]PF07654e3cfkH2 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07654ECOD (1.6)
B [auth H]PF07686e3cfkH1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07686ECOD (1.6)
D [auth B]PF07654e3cfkB2 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07654ECOD (1.6)
D [auth B]PF07686e3cfkB1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07686ECOD (1.6)
F [auth D]PF07654e3cfkD2 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07654ECOD (1.6)
F [auth D]PF07686e3cfkD1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07686ECOD (1.6)
H [auth F]PF07654e3cfkF2 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07654ECOD (1.6)
H [auth F]PF07686e3cfkF1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07686ECOD (1.6)
J [auth I]PF07654e3cfkI2 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07654ECOD (1.6)
J [auth I]PF07686e3cfkI1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07686ECOD (1.6)
L [auth K]PF07654e3cfkK2 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07654ECOD (1.6)
L [auth K]PF07686e3cfkK1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07686ECOD (1.6)
NPF07654e3cfkN2 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07654ECOD (1.6)
NPF07686e3cfkN1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07686ECOD (1.6)
PPF07654e3cfkP2 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07654ECOD (1.6)
PPF07686e3cfkP1 A: beta sandwichesX: Immunoglobulin-like beta-sandwichH: Immunoglobulin-relatedT: Immunoglobulin/Fibronectin type III/E set domains/PapD-likeF: PF07686ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

IMGT Antibody Annotation IMGT Database Homepage

ChainProtein NameDescriptionOrganism NameGene Allele Name(s)Domain Name(s)Receptor TypeReceptor DescriptionProvenance Source
34E4 Fab V-LAMBDA-C-KAPPA Chimeric (chimeric) IGLV1*01, IGKJ1*01, IGKJ2*01, IGKC*01 V-DOMAIN V-LAMBDA, C-DOMAIN C-KAPPA IG FAB-GAMMA-1_V-LAMBDA-C-KAPPA IMGT (202416-0)
34E4 Fab VH-CH1 Chimeric (chimeric) IGHV4-1*02, IGHJ4*01, IGHG1*01, IGHG1*02, IGHG1*04, IGHG1*05 V-DOMAIN VH, C-DOMAIN CH1 IG FAB-GAMMA-1_V-LAMBDA-C-KAPPA IMGT (202416-0)

SAbDab Antibody Annotation SAbDab Database Homepage

ChainChain ClassChain SubclassChain TypeAntigen Name(s) Provenance Source
Light ChainIGLV1 Lambda2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOLSAbDab (2024-04-26)
Heavy ChainIGHV4 -2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOLSAbDab (2024-04-26)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
PF07686Immunoglobulin V-set domain (V-set)Immunoglobulin V-set domainThis domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.Domain
PF07654Immunoglobulin C1-set domain (C1-set)Immunoglobulin C1-set domain- Domain
PF07686Immunoglobulin V-set domain (V-set)Immunoglobulin V-set domainThis domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.Domain
PF07654Immunoglobulin C1-set domain (C1-set)Immunoglobulin C1-set domain- Domain

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
IPR003597Immunoglobulin C1-setDomain
IPR013783Immunoglobulin-like foldHomologous Superfamily
IPR036179Immunoglobulin-like domain superfamilyHomologous Superfamily
IPR003599Immunoglobulin subtypeDomain
IPR013106Immunoglobulin V-set domainDomain
IPR007110Immunoglobulin-like domainDomain
IPR003006Immunoglobulin/major histocompatibility complex, conserved siteConserved Site
IPR003597Immunoglobulin C1-setDomain
IPR013783Immunoglobulin-like foldHomologous Superfamily
IPR036179Immunoglobulin-like domain superfamilyHomologous Superfamily
IPR003599Immunoglobulin subtypeDomain
IPR013106Immunoglobulin V-set domainDomain
IPR007110Immunoglobulin-like domainDomain
IPR003006Immunoglobulin/major histocompatibility complex, conserved siteConserved Site