4YR6 | pdb_00004yr6

Fab fragment of 5G6 in complex with epitope 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
Pharos: Disease Associations
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	e4yr6B1	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	e4yr6B2	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)
E	C1-set_4	e4yr6E2	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)
E	V-set	e4yr6E1	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	e4yr6A1	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	e4yr6A2	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)
D	V-set_8	e4yr6D2	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)
D	C1-set_1	e4yr6D1	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)
E	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)
D	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, E	5G6 Fab	L-KAPPA	Mus musculus (house mouse)	IGKV12-4102, IGKV12-4101, IGKJ101, IGKC01, IGKC*02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202546-0)
A, D	5G6 Fab	VH-CH1	Mus musculus (house mouse)	IGHV8-801, IGHJ101, IGHJ102, IGHG101	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202546-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B, E	Light Chain	IGKV12	Kappa	ace-lys-leu-arg-gly-val-leu-gln-gly-his-leu	SAbDab (2025-11-28)
A, D	Heavy Chain	IGHV8	-	ace-lys-leu-arg-gly-val-leu-gln-gly-his-leu	SAbDab (2025-11-28)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, E	light chain of 5G6	-	-	-
C, F	ACE-LYS-LEU-ARG-GLY-VAL-LEU-GLN-GLY-HIS-LEU	peptide receptor activity molecular transducer activity G protein-coupled receptor activity thrombin-activated receptor activity proteinase-activated receptor activity G protein-coupled peptide receptor activity signaling receptor activity transmembrane signaling receptor activity	multicellular organismal process regulation of body fluid levels wound healing response to stimulus hemostasis biological regulation blood coagulation response to stress coagulation regulation of biological quality response to wounding developmental process cellular developmental process hemopoiesis multicellular organismal process regulation of body fluid levels wound healing response to stimulus hemostasis biological regulation blood coagulation response to stress coagulation regulation of biological quality response to wounding developmental process cellular developmental process hemopoiesis megakaryocyte differentiation cell development myeloid cell differentiation cell differentiation megakaryocyte development anatomical structure development myeloid cell development cellular process regulation of response to external stimulus negative regulation of biological process regulation of response to wounding regulation of coagulation regulation of response to stress regulation of multicellular organismal process regulation of hemostasis regulation of biological process negative regulation of response to stimulus negative regulation of wound healing regulation of blood coagulation negative regulation of blood coagulation response to external stimulus negative regulation of response to wounding negative regulation of hemostasis fibrinolysis negative regulation of coagulation regulation of response to stimulus negative regulation of response to external stimulus regulation of wound healing negative regulation of multicellular organismal process cell activation platelet activation cellular response to stimulus regulation of cellular process cell surface receptor signaling pathway signaling signal transduction cell communication anatomical structure morphogenesis cell morphogenesis regulation of localization cellular localization inorganic ion homeostasis intracellular calcium ion homeostasis transport homeostatic process monoatomic ion transmembrane transport calcium ion homeostasis negative regulation of sequestering of calcium ion calcium ion transport metal ion transport maintenance of location in cell monoatomic cation transmembrane transport localization intracellular monoatomic cation homeostasis monoatomic ion homeostasis negative regulation of cellular process monoatomic ion transport intracellular chemical homeostasis monoatomic cation homeostasis monoatomic cation transport regulation of sequestering of calcium ion intracellular monoatomic ion homeostasis calcium ion transmembrane import into cytosol sequestering of calcium ion establishment of localization maintenance of location transmembrane transport release of sequestered calcium ion into cytosol cellular homeostasis chemical homeostasis calcium ion transmembrane transport cell adhesion protein maturation blood coagulation, intrinsic pathway blood coagulation, fibrin clot formation protein metabolic process protein activation cascade primary metabolic process gene expression macromolecule biosynthetic process biosynthetic process metabolic process macromolecule metabolic process positive regulation of biological process regulation of cell activation positive regulation of platelet activation positive regulation of cell activation positive regulation of cellular process regulation of platelet activation positive regulation of multicellular organismal process	cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle extracellular matrix external encapsulating structure protein-containing complex plasma membrane protein complex membrane protein complex glycoprotein Ib-IX-V complex receptor complex glycoprotein complex plasma membrane signaling receptor complex
A, D	heavy chain of 5G6	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C, F	IPR000372	Leucine-rich repeat N-terminal domain	Domain
C, F	IPR003591	Leucine-rich repeat, typical subtype	Repeat
C, F	IPR001611	Leucine-rich repeat	Repeat
C, F	IPR032675	Leucine-rich repeat domain superfamily	Homologous Superfamily
C, F	IPR000483	Cysteine-rich flanking region, C-terminal	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C, F	Pharos: P07359	Bernard-Soulier syndrome Bernard-Soulier syndrome, type A2, autosomal dominant pseudo-von Willebrand disease nonarteritic anterior ischemic optic neuropathy, susceptibility to thrombotic disease hypertensive disorder Von Willebrand disease, platelet type attention deficit hyperactivity disorder, inattentive type brain aneurysm hereditary von Willebrand disease non-arteritic anterior ischemic optic neuropathy thrombocytopenia osteosarcoma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
C, F	ACE	RESID: AA0041 , AA0042 , AA0043 , AA0044 , AA0045 , AA0046 , AA0049 , AA0050 , AA0051 , AA0052 , AA0053 , AA0054 , AA0354 PSI-MOD : N-acetyl-L-alanine MOD:00050 , N-acetyl-L-aspartic acid MOD:00051 , N-acetyl-L-cysteine MOD:00052 , N-acetyl-S-archeol-cysteine MOD:00897 , N-acetyl-L-glutamic acid MOD:00053 , N-acetyl-L-glutamine MOD:00054 , N-acetylglycine MOD:00055 , N-acetyl-L-methionine MOD:00058 , N-acetyl-L-proline MOD:00059 , N-acetyl-L-serine MOD:00060 , N,O-diacetylated L-serine MOD:00648 , N-acetyl-L-threonine MOD:00061 , N-acetyl-L-tyrosine MOD:00062 , N-acetyl-L-valine MOD:00063 , N2-acetyl-L-arginine MOD:00359

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.