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)
B [auth L]	Pyridoxal_deC	e5gisL1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Pyridoxal_deC	ECOD (v294.1)
A [auth H]	Pyridoxal_deC	e5gisH1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Pyridoxal_deC	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A [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
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 (202613-0)
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 (202613-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth L]	Light Chain	IGKV5	Kappa	thr-lys-pro-ile-thr-ile-gly-ser-his-ala-his-gly-asp-gln-tyr-lys	SAbDab (2026-04-10)
A [auth H]	Heavy Chain	IGHV1	-	thr-lys-pro-ile-thr-ile-gly-ser-his-ala-his-gly-asp-gln-tyr-lys	SAbDab (2026-04-10)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
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	nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process primary metabolic process nucleotide metabolic process NADP+ metabolic process purine-containing compound 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 metabolic process cellular process nucleoside phosphate metabolic process nicotinamide nucleotide metabolic process primary metabolic process nucleotide metabolic process NADP+ metabolic process purine-containing compound 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 metabolic process cellular process small molecule metabolic process phosphorus metabolic process aerobic respiration cellular respiration tricarboxylic acid cycle energy derivation by oxidation of organic compounds 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 monocarboxylic acid metabolic process secondary alcohol metabolic process isocitrate metabolic process tricarboxylic acid metabolic process alcohol metabolic process multicellular organismal process regulation of cellular process cellular developmental process regulation of developmental process negative regulation of biological process cell development regulation of neurogenesis regulation of cell differentiation regulation of gliogenesis negative regulation of glial cell proliferation regulation of cell development regulation of nervous system development neurogenesis multicellular organism development negative regulation of neurogenesis regulation of glial cell proliferation gliogenesis cell differentiation anatomical structure development negative regulation of cellular process regulation of multicellular organismal process negative regulation of nervous system development negative regulation of cell differentiation system development developmental process regulation of multicellular organismal development regulation of biological process negative regulation of cell population proliferation cell population proliferation negative regulation of developmental process biological regulation nervous system development negative regulation of gliogenesis negative regulation of cell development regulation of cell population proliferation glial cell proliferation negative regulation of multicellular organismal process NADP+ biosynthetic process nucleotide biosynthetic process purine-containing compound biosynthetic process pyridine nucleotide biosynthetic process pyridine-containing compound biosynthetic process nucleobase-containing compound biosynthetic process nicotinamide nucleotide biosynthetic process biosynthetic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process purine nucleotide biosynthetic process negative regulation of locomotion negative regulation of glial cell migration regulation of cell motility glial cell migration regulation of glial cell migration regulation of cell migration cell migration cell motility locomotion negative regulation of cell migration regulation of locomotion negative regulation of cell motility negative regulation of protein transport regulation of localization establishment of protein localization regulation of protein localization transport matrix metallopeptidase secretion negative regulation of transport protein localization to extracellular region localization secretion by cell regulation of secretion by cell negative regulation of secretion negative regulation of secretion by cell intracellular protein localization negative regulation of protein localization regulation of matrix metallopeptidase secretion secretion regulation of transport negative regulation of matrix metallopeptidase secretion establishment of protein localization to extracellular region regulation of establishment of protein localization export from cell negative regulation of establishment of protein localization regulation of protein transport protein secretion establishment of localization regulation of protein secretion regulation of secretion negative regulation of protein secretion protein transport macromolecule localization 2-oxoglutarate metabolic process dicarboxylic acid 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 vesicle extracellular membrane-bounded organelle 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 vesicle extracellular membrane-bounded organelle peroxisome microbody cytosol membrane-enclosed lumen mitochondrial matrix intracellular organelle lumen organelle lumen
B [auth L]	Light chain of Fab fragment	-	-	-
A [auth H]	Heavy chain of Fab fragment	-	-	-

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 gemistocytic astrocytoma Neoplasm Recurrence, Local 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 gemistocytic astrocytoma Neoplasm Recurrence, Local 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 epithelioid hemangioma mature T-cell and NK-cell non-Hodgkin lymphoma childhood oligodendroglioma hypertrophic cardiomyopathy intrahepatic cholangiocarcinoma anaplastic oligoastrocytoma bone disease breast carcinoma subependymoma genetic endocrine growth disease tuberculosis osteoarthritis hematopoietic and lymphoid system neoplasm inborn errors of metabolism osteosarcoma D-2-hydroxyglutaric aciduria dilated cardiomyopathy alopecia pancreatic intraductal papillary-mucinous neoplasm ependymoma lung adenocarcinoma astrocytoma (excluding glioblastoma) malignant ependymoma bile duct cancer myelofibrosis brain disease cancer glioblastoma glioma susceptibility 1 osteoarthritis susceptibility 1 congenital anemia D-2-hydroxyglutaric aciduria 1 intellectual disability ovarian cancer 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 gastric carcinoma breast cancer spinal cord disease non-small cell lung carcinoma glioma hematologic disease acne 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.