5XV5 | pdb_00005xv5

Crystal structure of Rib7 mutant S88E from Methanosarcina mazei

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)
F	d5xv5f_	Alpha and beta proteins (a/b)	Dihydrofolate reductase-like	Dihydrofolate reductase-like	automated matches	automated matches	(Methanosarcina mazei Go1 ) [TaxId: 192952 ],	SCOPe (2.08)
E	d5xv5e_	Alpha and beta proteins (a/b)	Dihydrofolate reductase-like	Dihydrofolate reductase-like	automated matches	automated matches	(Methanosarcina mazei Go1 ) [TaxId: 192952 ],	SCOPe (2.08)
D	d5xv5d1	Alpha and beta proteins (a/b)	Dihydrofolate reductase-like	Dihydrofolate reductase-like	automated matches	automated matches	(Methanosarcina mazei Go1 ) [TaxId: 192952 ],	SCOPe (2.08)
D	d5xv5d2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Methanosarcina mazei Go1 ) [TaxId: 192952 ],	SCOPe (2.08)
C	d5xv5c_	Alpha and beta proteins (a/b)	Dihydrofolate reductase-like	Dihydrofolate reductase-like	automated matches	automated matches	(Methanosarcina mazei Go1 ) [TaxId: 192952 ],	SCOPe (2.08)
B	d5xv5b_	Alpha and beta proteins (a/b)	Dihydrofolate reductase-like	Dihydrofolate reductase-like	automated matches	automated matches	(Methanosarcina mazei Go1 ) [TaxId: 192952 ],	SCOPe (2.08)
A	d5xv5a1	Alpha and beta proteins (a/b)	Dihydrofolate reductase-like	Dihydrofolate reductase-like	automated matches	automated matches	(Methanosarcina mazei Go1 ) [TaxId: 192952 ],	SCOPe (2.08)
A	d5xv5a2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Methanosarcina mazei Go1 ) [TaxId: 192952 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	Dihydrofolate reductase-like	8085867	3001255	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Dihydrofolate reductase-like	8085867	3001255	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Dihydrofolate reductase-like	8085867	3001255	SCOP2B (2022-06-29)
C	SCOP2 Family	RibD C-terminal domain-like	8085866	4003207	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Dihydrofolate reductase-like	8085867	3001255	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	Dihydrofolate reductase-like	8085867	3001255	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Dihydrofolate reductase-like	8085867	3001255	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)
F	RibD_C	e5xv5F1	A: a/b three-layered sandwiches	X: Dihydrofolate reductases (From Topology)	H: Dihydrofolate reductases (From Topology)	T: Dihydrofolate reductases	F: RibD_C	ECOD (1.6)
E	RibD_C	e5xv5E1	A: a/b three-layered sandwiches	X: Dihydrofolate reductases (From Topology)	H: Dihydrofolate reductases (From Topology)	T: Dihydrofolate reductases	F: RibD_C	ECOD (1.6)
D	RibD_C	e5xv5D1	A: a/b three-layered sandwiches	X: Dihydrofolate reductases (From Topology)	H: Dihydrofolate reductases (From Topology)	T: Dihydrofolate reductases	F: RibD_C	ECOD (1.6)
C	RibD_C	e5xv5C1	A: a/b three-layered sandwiches	X: Dihydrofolate reductases (From Topology)	H: Dihydrofolate reductases (From Topology)	T: Dihydrofolate reductases	F: RibD_C	ECOD (1.6)
B	RibD_C	e5xv5B1	A: a/b three-layered sandwiches	X: Dihydrofolate reductases (From Topology)	H: Dihydrofolate reductases (From Topology)	T: Dihydrofolate reductases	F: RibD_C	ECOD (1.6)
A	RibD_C	e5xv5A1	A: a/b three-layered sandwiches	X: Dihydrofolate reductases (From Topology)	H: Dihydrofolate reductases (From Topology)	T: Dihydrofolate reductases	F: RibD_C	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	3.40.430.10	Alpha Beta	3-Layer(aba) Sandwich	Dihydrofolate Reductase, subunit A	Dihydrofolate Reductase, subunit A	CATH (4.3.0)
E	3.40.430.10	Alpha Beta	3-Layer(aba) Sandwich	Dihydrofolate Reductase, subunit A	Dihydrofolate Reductase, subunit A	CATH (4.3.0)
D	3.40.430.10	Alpha Beta	3-Layer(aba) Sandwich	Dihydrofolate Reductase, subunit A	Dihydrofolate Reductase, subunit A	CATH (4.3.0)
C	3.40.430.10	Alpha Beta	3-Layer(aba) Sandwich	Dihydrofolate Reductase, subunit A	Dihydrofolate Reductase, subunit A	CATH (4.3.0)
B	3.40.430.10	Alpha Beta	3-Layer(aba) Sandwich	Dihydrofolate Reductase, subunit A	Dihydrofolate Reductase, subunit A	CATH (utative)
A	3.40.430.10	Alpha Beta	3-Layer(aba) Sandwich	Dihydrofolate Reductase, subunit A	Dihydrofolate Reductase, subunit A	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF01872	RibD C-terminal domain (RibD_C)	RibD C-terminal domain	The function of this domain is not known, but it is thought to be involved in riboflavin biosynthesis. This domain is found in the C terminus of RibD/RibG Swiss:P25539, in combination with Pfam:PF00383, as well as in isolation in some archaebacterial ...	The function of this domain is not known, but it is thought to be involved in riboflavin biosynthesis. This domain is found in the C terminus of RibD/RibG Swiss:P25539, in combination with Pfam:PF00383, as well as in isolation in some archaebacterial proteins Swiss:P95872. This family appears to be related to Pfam:PF00186.	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	Conserved protein	5-amino-6-(5-phosphoribosylamino)uracil reductase activity oxidoreductase activity oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on CH-OH group of donors catalytic activity binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding nucleotide binding heterocyclic compound binding NADP binding small molecule binding	water-soluble vitamin biosynthetic process small molecule biosynthetic process flavin-containing compound metabolic process vitamin biosynthetic process riboflavin biosynthetic process vitamin metabolic process flavin-containing compound biosynthetic process biosynthetic process metabolic process cellular process small molecule metabolic process riboflavin metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR024072	Dihydrofolate reductase-like domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR006401	2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine 1-reductase, archaeal	Family
A, B, C, D, E A, B, C, D, E, F	IPR050765	Riboflavin Biosynthesis HTP Reductase	Family
A, B, C, D, E A, B, C, D, E, F	IPR011549	Riboflavin-specific deaminase, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F	IPR002734	Bacterial bifunctional deaminase-reductase, C-terminal	Domain

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.