4BKL | pdb_00004bkl

Crystal structure of the arthritogenic antibody M2139 (Fab fragment) in complex with the triple-helical J1 peptide

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	C1-set_4	e4bklB1	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)
B	V-set	e4bklB2	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)
A	V-set_8	e4bklA2	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)
A	C1-set_1	e4bklA1	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)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A	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
B	M2139 Fab	L-KAPPA	Mus musculus (house mouse)	IGKV3-101, IGKJ201, IGKC01, IGKC02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-2B_KAPPA	IMGT (202549-0)
A	M2139 Fab	VH-CH1	Mus musculus (house mouse)	IGHV1-701, IGHV1-401, IGHJ201, IGHG2B02	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-2B_KAPPA	IMGT (202549-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B	Light Chain	IGKV3	Kappa	j1 epitope \| j1 epitope \| j1 epitope	SAbDab (2025-12-19)
A	Heavy Chain	IGHV1	-	j1 epitope \| j1 epitope \| j1 epitope	SAbDab (2025-12-19)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth E], D [auth F], E [auth G]	J1 EPITOPE	protein binding binding signaling receptor binding MHC class II protein binding MHC protein binding structural molecule activity extracellular matrix structural constituent identical protein binding protein homodimerization activity protein dimerization activity platelet-derived growth factor binding growth factor binding proteoglycan binding carbohydrate derivative binding protein binding binding signaling receptor binding MHC class II protein binding MHC protein binding structural molecule activity extracellular matrix structural constituent identical protein binding protein homodimerization activity protein dimerization activity platelet-derived growth factor binding growth factor binding proteoglycan binding carbohydrate derivative binding cation binding ion binding metal ion binding small molecule binding	developmental process multicellular organism development multicellular organismal process skeletal system development connective tissue development anatomical structure development animal organ development tissue development cartilage development system development carbohydrate derivative metabolic process metabolic process cellular process primary metabolic process developmental process multicellular organism development multicellular organismal process skeletal system development connective tissue development anatomical structure development animal organ development tissue development cartilage development system development carbohydrate derivative metabolic process metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process proteoglycan metabolic process glycoprotein metabolic process limb development appendage development limb bud formation anatomical structure morphogenesis appendage morphogenesis anatomical structure formation involved in morphogenesis limb morphogenesis cellular response to stimulus negative regulation of extrinsic apoptotic signaling pathway in absence of ligand regulation of cellular process response to stimulus signal transduction in absence of ligand negative regulation of signaling signaling negative regulation of biological process regulation of signal transduction regulation of programmed cell death negative regulation of cell communication extrinsic apoptotic signaling pathway negative regulation of signal transduction in absence of ligand cell communication negative regulation of extrinsic apoptotic signaling pathway negative regulation of apoptotic signaling pathway negative regulation of cellular process extrinsic apoptotic signaling pathway in absence of ligand signal transduction regulation of signaling regulation of biological process cell surface receptor signaling pathway negative regulation of response to stimulus negative regulation of programmed cell death regulation of apoptotic process biological regulation cell death negative regulation of signal transduction regulation of extrinsic apoptotic signaling pathway apoptotic signaling pathway negative regulation of apoptotic process regulation of response to stimulus regulation of extrinsic apoptotic signaling pathway in absence of ligand regulation of cell communication apoptotic process programmed cell death regulation of apoptotic signaling pathway central nervous system development nervous system development epithelium development otic vesicle development ear development sensory organ development tube development inner ear development embryonic skeletal joint development embryonic organ morphogenesis chordate embryonic development embryonic morphogenesis embryo development embryonic skeletal joint morphogenesis embryo development ending in birth or egg hatching embryonic skeletal system development animal organ morphogenesis skeletal system morphogenesis embryonic organ development embryonic skeletal system morphogenesis ear morphogenesis sensory organ morphogenesis inner ear morphogenesis regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process regulation of metabolic process bone development endochondral ossification replacement ossification endochondral bone morphogenesis ossification bone morphogenesis cell aggregation cartilage condensation cellular component organization collagen fibril organization extracellular matrix organization cellular component organization or biogenesis extracellular structure organization external encapsulating structure organization heart development heart morphogenesis circulatory system development notochord development system process sensory perception nervous system process sensory perception of sound sensory perception of mechanical stimulus sensory perception of light stimulus visual perception multicellular organismal-level homeostasis homeostatic process anatomical structure homeostasis tissue homeostasis cartilage development involved in endochondral bone morphogenesis cellular developmental process cell differentiation chondrocyte differentiation roof of mouth development anterior head development head development cellular response to BMP stimulus cellular response to endogenous stimulus response to BMP cellular response to growth factor stimulus response to endogenous stimulus response to growth factor	protein-containing complex collagen trimer basement membrane cell periphery extracellular matrix cellular anatomical structure external encapsulating structure solid phase of interstitial matrix fibrillar collagen trimer complex of collagen trimers fibrillar collagen collagen type XI trimer supramolecular complex collagenous component of interstitial matrix protein-containing complex collagen trimer basement membrane cell periphery extracellular matrix cellular anatomical structure external encapsulating structure solid phase of interstitial matrix fibrillar collagen trimer complex of collagen trimers fibrillar collagen collagen type XI trimer supramolecular complex collagenous component of interstitial matrix interstitial matrix collagen type II trimer intracellular anatomical structure cytoplasm extracellular region extracellular space
B	M2139 FAB FRAGMENT LIGHT CHAIN	-	-	-
A	M2139 FAB FRAGMENT HEAVY CHAIN	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth E], D [auth F], E [auth G]	IPR008160	Collagen triple helix repeat	Repeat
C [auth E], D [auth F], E [auth G]	IPR000885	Fibrillar collagen, C-terminal	Domain
C [auth E], D [auth F], E [auth G]	IPR001007	VWFC domain	Domain
C [auth E], D [auth F], E [auth G]	IPR050149	Collagen superfamily	Family

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
C [auth E], D [auth F], E [auth G]	HYP	Parent Component: PRO RESID: AA0030 PSI-MOD : 4-hydroxy-L-proline MOD:00039

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.