7PHQ | pdb_00007phq

Structure of homo-dimeric Staphylococcus capitis divalent metal ion transporter (DMT) by NabFab-fiducial assisted cryo-EM

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD
Membrane Protein Annotation: mpstruc

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth B]	SCOP2B Superfamily	SNF-like	8104211	3001654	SCOP2B (2022-06-29)
H [auth D]	SCOP2B Superfamily	SNF-like	8104211	3001654	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)
C [auth B]	Nramp	e7phqB1	A: alpha complex topology	X: Sodium:neurotransmitter symporter family (SNF)-like (From Topology)	H: Sodium:neurotransmitter symporter family (SNF)-like (From Topology)	T: Sodium:neurotransmitter symporter family (SNF)-like	F: Nramp	ECOD (1.6)
H [auth D]	Nramp	e7phqD1	A: alpha complex topology	X: Sodium:neurotransmitter symporter family (SNF)-like (From Topology)	H: Sodium:neurotransmitter symporter family (SNF)-like (From Topology)	T: Sodium:neurotransmitter symporter family (SNF)-like	F: Nramp	ECOD (1.6)
A [auth H]	C1-set_1	e7phqH2	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)
A [auth H]	V-set_12	e7phqH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
F [auth A]	C1-set_1	e7phqA2	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)
F [auth A]	V-set_12	e7phqA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
B [auth L]	C1-set_4	e7phqL2	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	e7phqL1	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)
G [auth C]	C1-set_4	e7phqC2	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)
G [auth C]	V-set	e7phqC1	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)
D [auth N]	V-set_8	e7phqN1	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)
I [auth E]	V-set_8	e7phqE1	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)
E [auth K]	V-set_12	e7phqK1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
J [auth F]	V-set_12	e7phqF1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
A [auth H], F [auth A]	Heavy Chain	IGHV3	-	-	SAbDab (2025-05-16)
B [auth L], G [auth C]	Light Chain	IGKV1	Kappa	-	SAbDab (2025-05-16)
D [auth N], I [auth E]	Heavy Chain	IGHV1	-	divalent metal cation transporter mnth	SAbDab (2025-05-16)
E [auth K], J [auth F]	Heavy Chain	IGHV1	-	-	SAbDab (2025-05-16)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth B], H [auth D]	PF01566	Natural resistance-associated macrophage protein-like (Nramp)	Natural resistance-associated macrophage protein-like	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth B], H [auth D]	Divalent metal cation transporter MntH	monoatomic cation transmembrane transporter activity manganese ion transmembrane transporter activity inorganic molecular entity transmembrane transporter activity inorganic cation transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transition metal ion transmembrane transporter activity metal ion transmembrane transporter activity transmembrane transporter activity cadmium ion transmembrane transporter activity active transmembrane transporter activity symporter activity secondary active transmembrane transporter activity cation binding monoatomic cation transmembrane transporter activity manganese ion transmembrane transporter activity inorganic molecular entity transmembrane transporter activity inorganic cation transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transition metal ion transmembrane transporter activity metal ion transmembrane transporter activity transmembrane transporter activity cadmium ion transmembrane transporter activity active transmembrane transporter activity symporter activity secondary active transmembrane transporter activity cation binding ion binding binding metal ion binding small molecule binding	transport monoatomic ion transmembrane transport iron ion transport iron ion transmembrane transport inorganic ion transmembrane transport establishment of localization metal ion transport inorganic cation transmembrane transport transmembrane transport monoatomic cation transmembrane transport localization transition metal ion transport monoatomic ion transport cellular process transport monoatomic ion transmembrane transport iron ion transport iron ion transmembrane transport inorganic ion transmembrane transport establishment of localization metal ion transport inorganic cation transmembrane transport transmembrane transport monoatomic cation transmembrane transport localization transition metal ion transport monoatomic ion transport cellular process monoatomic cation transport	cell periphery cellular anatomical structure plasma membrane membrane
A [auth H], F [auth A]	NabFab HC	-	-	-
B [auth L], G [auth C]	NabFab LC	-	-	-
D [auth N], I [auth E]	DMT-Nb16_4	-	-	-
E [auth K], J [auth F]	Anti-Fab nanobody	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth B], H [auth D]	IPR001046	NRAMP family	Family

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
C [auth B], H [auth D]	OPM	Transmembrane	Alpha-helical polytopic	APC (Amino acid-Polyamine-organoCation) superfamily	Divalent metal ion transporter (NRAMP)

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
C [auth B], H [auth D]	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
C [auth B], H [auth D]	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
C [auth B], H [auth D]	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Solute Carrier (SLC) Transporter Superfamily	divalent metal ion transporter (DMT), monomer

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.