3MD9 | pdb_00003md9

Structure of apo form of a periplasmic heme binding protein

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d3md9b_	Alpha and beta proteins (a/b)	Chelatase-like	'Helical backbone' metal receptor	automated matches	automated matches	(Yersinia pestis ) [TaxId: 632 ],	SCOPe (2.08)
A	d3md9a_	Alpha and beta proteins (a/b)	Chelatase-like	'Helical backbone' metal receptor	automated matches	automated matches	(Yersinia pestis ) [TaxId: 632 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	YadA_stalk	e3md9B1	A: a/b three-layered sandwiches	X: SMI1/KNR4-like	H: SMI1/KNR4-like	T: SMI1/KNR4-like	F: YadA_stalk	ECOD (v294.1)
A	YadA_stalk	e3md9A1	A: a/b three-layered sandwiches	X: SMI1/KNR4-like	H: SMI1/KNR4-like	T: SMI1/KNR4-like	F: YadA_stalk	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.40.50.1980	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nitrogenase molybdenum iron protein domain	CATH (4.3.0)
A	3.40.50.1980	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Nitrogenase molybdenum iron protein domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01497	Periplasmic binding protein (Peripla_BP_2)	Periplasmic binding protein	This is sensor domain found in bacterial periplasmic binding proteins, several of which are involved in iron and cobalamin transport [1,2,3]. Among its ligands are siderophores bacillibactin, enterobactin and iron(III)-hydroxamates (Matilla et. al., ...	This is sensor domain found in bacterial periplasmic binding proteins, several of which are involved in iron and cobalamin transport [1,2,3]. Among its ligands are siderophores bacillibactin, enterobactin and iron(III)-hydroxamates (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1 https://doi.org/10.1093/femsre/fuab043).	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Hemin-binding periplasmic protein hmuT	-	localization transport iron ion transport transition metal ion transport monoatomic ion transport monoatomic cation transport establishment of localization metal ion transport	cellular anatomical structure extracellular region periplasmic space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR002491	ABC transporter periplasmic binding domain	Domain
A, B	IPR050902	ABC Transporter Solute-Binding	Family

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.