5VDF | pdb_00005vdf

Crystal Structure of Cu(I)-loaded yeast Atx1: Crystal Form II

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 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)
H	d5vdfh_	Alpha and beta proteins (a+b)	Ferredoxin-like	HMA, heavy metal-associated domain	HMA, heavy metal-associated domain	ATX1 metallochaperone protein (ATOX1)	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
G	d5vdfg_	Alpha and beta proteins (a+b)	Ferredoxin-like	HMA, heavy metal-associated domain	HMA, heavy metal-associated domain	ATX1 metallochaperone protein (ATOX1)	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
F	d5vdff_	Alpha and beta proteins (a+b)	Ferredoxin-like	HMA, heavy metal-associated domain	HMA, heavy metal-associated domain	ATX1 metallochaperone protein (ATOX1)	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
E	d5vdfe_	Alpha and beta proteins (a+b)	Ferredoxin-like	HMA, heavy metal-associated domain	HMA, heavy metal-associated domain	ATX1 metallochaperone protein (ATOX1)	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
D	d5vdfd_	Alpha and beta proteins (a+b)	Ferredoxin-like	HMA, heavy metal-associated domain	HMA, heavy metal-associated domain	ATX1 metallochaperone protein (ATOX1)	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
C	d5vdfc_	Alpha and beta proteins (a+b)	Ferredoxin-like	HMA, heavy metal-associated domain	HMA, heavy metal-associated domain	ATX1 metallochaperone protein (ATOX1)	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
B	d5vdfb_	Alpha and beta proteins (a+b)	Ferredoxin-like	HMA, heavy metal-associated domain	HMA, heavy metal-associated domain	ATX1 metallochaperone protein (ATOX1)	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)
A	d5vdfa_	Alpha and beta proteins (a+b)	Ferredoxin-like	HMA, heavy metal-associated domain	HMA, heavy metal-associated domain	ATX1 metallochaperone protein (ATOX1)	Baker's yeast (Saccharomyces cerevisiae S288C ) [TaxId: 559292 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H	SCOP2B Superfamily	HMA, heavy metal-associated domain	8035500	3001159	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	HMA, heavy metal-associated domain	8035500	3001159	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	HMA, heavy metal-associated domain	8035500	3001159	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	HMA, heavy metal-associated domain	8035500	3001159	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	HMA, heavy metal-associated domain	8035500	3001159	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	HMA, heavy metal-associated domain	8035500	3001159	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	HMA, heavy metal-associated domain	8035500	3001159	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	HMA, heavy metal-associated domain	8035500	3001159	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)
H	SAM_KSR1_N	e5vdfH1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: SAM_KSR1_N	ECOD (develop294)
G	SAM_KSR1_N	e5vdfG1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: SAM_KSR1_N	ECOD (develop294)
F	SAM_KSR1_N	e5vdfF1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: SAM_KSR1_N	ECOD (develop294)
E	SAM_KSR1_N	e5vdfE1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: SAM_KSR1_N	ECOD (develop294)
D	SAM_KSR1_N	e5vdfD1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: SAM_KSR1_N	ECOD (develop294)
C	SAM_KSR1_N	e5vdfC1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: SAM_KSR1_N	ECOD (develop294)
B	SAM_KSR1_N	e5vdfB1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: SAM_KSR1_N	ECOD (develop294)
A	SAM_KSR1_N	e5vdfA1	A: alpha bundles	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: SAM_KSR1_N	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	3.30.70.100	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
G	3.30.70.100	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
F	3.30.70.100	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
E	3.30.70.100	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
D	3.30.70.100	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
C	3.30.70.100	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
B	3.30.70.100	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
A	3.30.70.100	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H	PF00403	Heavy-metal-associated domain (HMA)	Heavy-metal-associated domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H	Metal homeostasis factor ATX1	cation binding ion binding binding metal ion binding small molecule binding metallochaperone activity molecular carrier activity copper chaperone activity	intracellular iron ion homeostasis inorganic ion homeostasis cellular homeostasis chemical homeostasis homeostatic process intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis cellular response to stimulus response to oxidative stress cellular response to chemical stimulus response to stimulus intracellular iron ion homeostasis inorganic ion homeostasis cellular homeostasis chemical homeostasis homeostatic process intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis cellular response to stimulus response to oxidative stress cellular response to chemical stimulus response to stimulus cellular response to stress response to stress response to chemical cellular response to oxidative stress cellular process cellular response to chemical stress localization transport copper ion transport transition metal ion transport monoatomic ion transport monoatomic cation transport establishment of localization metal ion transport	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR017969	Heavy-metal-associated, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F, G, H	IPR006121	Heavy metal-associated domain, HMA	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR036163	Heavy metal-associated domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR051881	Copper transport ATOX1-like	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.