2PMV | pdb_00002pmv

Crystal Structure of Human Intrinsic Factor- Cobalamin Complex at 2.6 A Resolution

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Six-hairpin glycosidases	8051862	3000970	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Six-hairpin glycosidases	8051862	3000970	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Transcobalamin C-terminal domain-like	8051863	3002041	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Six-hairpin glycosidases	8051862	3000970	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Six-hairpin glycosidases	8051862	3000970	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Transcobalamin C-terminal domain-like	8051863	3002041	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	MreC	e2pmvD1	A: alpha bundles	X: DEATH domain	H: HTH	T: winged helix domain	F: MreC	ECOD (develop294)
C	Rpf1_C	e2pmvC2	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: Rpf1_C	ECOD (develop294)
C	Cobalamin_bind	e2pmvC3	A: alpha bundles	X: RuvA-C	H: post-HMGL domain-like	T: post-HMGL domain-like	F: Cobalamin_bind	ECOD (develop294)
B	MreC	e2pmvB1	A: alpha bundles	X: DEATH domain	H: HTH	T: winged helix domain	F: MreC	ECOD (develop294)
A	Rpf1_C	e2pmvA2	A: alpha bundles	X: HTH	H: Nudix	T: Nudix	F: Rpf1_C	ECOD (develop294)
A	Cobalamin_bind	e2pmvA3	A: alpha bundles	X: RuvA-C	H: post-HMGL domain-like	T: post-HMGL domain-like	F: Cobalamin_bind	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	1.50.10.20	Mainly Alpha	Alpha/alpha barrel	Glycosyltransferase		CATH (4.3.0)
C	1.50.10.20	Mainly Alpha	Alpha/alpha barrel	Glycosyltransferase		CATH (4.3.0)
C	2.170.130.30	Mainly Beta	Beta Complex	Ferric Hydroxamate Uptake Protein	Chain A, domain 1	CATH (4.3.0)
B	1.50.10.20	Mainly Alpha	Alpha/alpha barrel	Glycosyltransferase		CATH (4.3.0)
A	1.50.10.20	Mainly Alpha	Alpha/alpha barrel	Glycosyltransferase		CATH (4.3.0)
A	2.170.130.30	Mainly Beta	Beta Complex	Ferric Hydroxamate Uptake Protein	Chain A, domain 1	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Gastric intrinsic factor	molecular carrier activity protein binding binding cargo receptor ligand activity vitamin binding cobalamin binding tetrapyrrole binding heterocyclic compound binding small molecule binding	localization nitrogen compound transport transport vitamin transport cobalamin transport establishment of localization monoatomic ion transmembrane transport metal ion transport cobalt ion transport monoatomic cation transmembrane transport transmembrane transport transition metal ion transport monoatomic ion transport cellular process localization nitrogen compound transport transport vitamin transport cobalamin transport establishment of localization monoatomic ion transmembrane transport metal ion transport cobalt ion transport monoatomic cation transmembrane transport transmembrane transport transition metal ion transport monoatomic ion transport cellular process monoatomic cation transport	cell periphery cellular anatomical structure apical part of cell membrane plasma membrane plasma membrane region apical plasma membrane membrane-bounded organelle intracellular anatomical structure endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cell periphery cellular anatomical structure apical part of cell membrane plasma membrane plasma membrane region apical plasma membrane membrane-bounded organelle intracellular anatomical structure endosome intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle organelle cytoplasm vesicle extracellular region membrane-enclosed lumen lytic vacuole vacuolar lumen vacuole lysosomal lumen intracellular organelle lumen organelle lumen lysosome cell projection actin-based cell projection microvillus plasma membrane bounded cell projection extracellular space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR002157	Cobalamin (vitamin B12)-binding protein	Family
A, B, C, D	IPR051588	Eukaryotic Cobalamin Transport	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: P27352	congenital intrinsic factor deficiency schizophrenia bipolar disorder Crohn disease Congenital deficiency of intrinsic factor pernicious anemia

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.