5GIS | pdb_00005gis

Crystal structure of a Fab fragment with its ligand 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)
A [auth H]	V-set_8	e5gisH1	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 [auth H]	C1-set_1	e5gisH2	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 L]	C1-set_4	e5gisL1	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 [auth L]	V-set	e5gisL2	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B [auth L]	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
A [auth H]	Antibody Fab Fragment	VH-CH1	Mus musculus (house mouse)	IGHV1-6101, IGHJ201, IGHG2A01, IGHG2A02	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-2A_KAPPA	IMGT (202516-0)
B [auth L]	Antibody Fab Fragment	L-KAPPA	Mus musculus (house mouse)	IGKV5-4301, IGKJ202, IGKJ401, IGKC01, IGKC*02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-2A_KAPPA	IMGT (202516-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A [auth H]	Heavy Chain	IGHV1	-	thr-lys-pro-ile-thr-ile-gly-ser-his-ala-his-gly-asp-gln-tyr-lys	SAbDab (2025-05-02)
B [auth L]	Light Chain	IGKV5	Kappa	thr-lys-pro-ile-thr-ile-gly-ser-his-ala-his-gly-asp-gln-tyr-lys	SAbDab (2025-05-02)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth H]	Heavy chain of Fab fragment	-	-	-
B [auth L]	Light chain of Fab fragment	-	-	-
C	THR-LYS-PRO-ILE-THR-ILE-GLY-SER-HIS-ALA-HIS-GLY-ASP-GLN-TYR-LYS	cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding isocitrate dehydrogenase [NAD(P)+] activity oxidoreductase activity oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor isocitrate dehydrogenase (NADP+) activity oxidoreductase activity, acting on CH-OH group of donors catalytic activity NAD binding nucleoside phosphate binding cation binding magnesium ion binding ion binding binding metal ion binding small molecule binding isocitrate dehydrogenase [NAD(P)+] activity oxidoreductase activity oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor isocitrate dehydrogenase (NADP+) activity oxidoreductase activity, acting on CH-OH group of donors catalytic activity NAD binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding	aerobic respiration cellular respiration tricarboxylic acid cycle energy derivation by oxidation of organic compounds primary metabolic process metabolic process cellular process generation of precursor metabolites and energy carbohydrate metabolic process glyoxylate metabolic process glyoxylate cycle oxoacid metabolic process carboxylic acid metabolic process organic acid metabolic process aerobic respiration cellular respiration tricarboxylic acid cycle energy derivation by oxidation of organic compounds primary metabolic process metabolic process cellular process generation of precursor metabolites and energy carbohydrate metabolic process glyoxylate metabolic process glyoxylate cycle oxoacid metabolic process carboxylic acid metabolic process organic acid metabolic process aldehyde metabolic process small molecule metabolic process monocarboxylic acid metabolic process secondary alcohol metabolic process isocitrate metabolic process tricarboxylic acid metabolic process alcohol metabolic process 2-oxoglutarate metabolic process dicarboxylic acid metabolic process nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process nucleotide metabolic process purine-containing compound metabolic process NADP metabolic process nucleobase-containing compound metabolic process purine nucleotide metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process pyridine-containing compound metabolic process phosphorus metabolic process pyridine nucleotide metabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle peroxisome microbody cytosol membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C	IPR004790	Isocitrate dehydrogenase NADP-dependent	Family
C	IPR024084	Isopropylmalate dehydrogenase-like domain	Domain
C	IPR019818	Isocitrate/isopropylmalate dehydrogenase, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C	Pharos: P48735	Ollier disease cholangiocarcinoma 2-hydroxyglutaric aciduria chondroma Maffucci syndrome acute myeloid leukemia oligodendroglioma hemangioma oligoastrocytoma d-2-hydroxyglutaric aciduria 2 Neoplasm Recurrence, Local gemistocytic astrocytoma visual epilepsy osteoporosis acute promyelocytic leukemia Ollier disease cholangiocarcinoma 2-hydroxyglutaric aciduria chondroma Maffucci syndrome acute myeloid leukemia oligodendroglioma hemangioma oligoastrocytoma d-2-hydroxyglutaric aciduria 2 Neoplasm Recurrence, Local gemistocytic astrocytoma visual epilepsy osteoporosis acute promyelocytic leukemia intramuscular hemangioma kidney failure anaplastic oligodendroglioma placental hemangioma primary myelofibrosis fibrillary astrocytoma central nervous system disease hydronephrosis adult oligodendroglioma anaplastic astrocytoma angioimmunoblastic T-cell lymphoma protoplasmic astrocytoma mature T-cell and NK-cell non-Hodgkin lymphoma epithelioid hemangioma childhood oligodendroglioma hypertrophic cardiomyopathy intrahepatic cholangiocarcinoma anaplastic oligoastrocytoma bone disease breast carcinoma subependymoma genetic endocrine growth disease tuberculosis osteoarthritis hematopoietic and lymphoid system neoplasm osteosarcoma D-2-hydroxyglutaric aciduria inborn errors of metabolism alopecia pancreatic intraductal papillary-mucinous neoplasm dilated cardiomyopathy lung adenocarcinoma astrocytoma (excluding glioblastoma) ependymoma malignant ependymoma bile duct cancer myelofibrosis brain disease cancer glioblastoma glioma susceptibility 1 osteoarthritis susceptibility 1 congenital anemia ovarian cancer D-2-hydroxyglutaric aciduria 1 intellectual disability invasive ductal breast carcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia L-2-hydroxyglutaric aciduria plasma cell myeloma lung cancer biliary tract neoplasm breast cancer gastric carcinoma non-small cell lung carcinoma spinal cord disease glioma acne hematologic disease aleukemic leukemia pancreatic ductal adenocarcinoma ductal breast carcinoma in situ large cell medulloblastoma atypical teratoid rhabdoid tumor psoriasis

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
A [auth H]	PCA	Parent Component: GLN RESID: AA0031 PSI-MOD : 2-pyrrolidone-5-carboxylic acid (Gln) MOD:00040 , 2-pyrrolidone-5-carboxylic acid (Glu) MOD:00420

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.