1VK6
Crystal structure of NADH pyrophosphatase (1790429) from Escherichia coli k12 at 2.20 A resolution
Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage
Chains | Domain Info | Class | Fold | Superfamily | Family | Domain | Species | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
A | d1vk6a2 | Alpha and beta proteins (a+b) | Nudix | Nudix | NADH pyrophosphatase | NADH pyrophosphatase | (Escherichia coli K-12 ) [TaxId: 83333 ], | SCOPe (2.08) |
A | d1vk6a4 | Small proteins | Rubredoxin-like | NADH pyrophosphatase intervening domain | NADH pyrophosphatase intervening domain | NADH pyrophosphatase intervening domain | (Escherichia coli K-12 ) [TaxId: 83333 ], | SCOPe (2.08) |
A | d1vk6a5 | Artifacts | Tags | Tags | Tags | N-terminal Tags | (Escherichia coli K-12 ) [TaxId: 83333 ], | SCOPe (2.08) |
Domain Annotation: SCOP2 Classification SCOP2 Database Homepage
Chains | Type | Family Name | Domain Identifier | Family Identifier | Provenance Source (Version) |
---|---|---|---|---|---|
A | SCOP2 Family | NADH pyrophosphatase | 8023632 | 4001557 | SCOP2 (2022-06-29) |
A | SCOP2 Family | NADH pyrophosphatase | 8029773 | 4001557 | SCOP2 (2022-06-29) |
A | SCOP2 Family | NADH pyrophosphatase intervening domain | 8029774 | 4002792 | SCOP2 (2022-06-29) |
A | SCOP2 Superfamily | Nudix | 8036012 | 3000098 | SCOP2 (2022-06-29) |
A | SCOP2 Superfamily | Nudix | 8042152 | 3000098 | SCOP2 (2022-06-29) |
A | SCOP2 Superfamily | NADH pyrophosphatase intervening domain | 8042153 | 3001752 | SCOP2 (2022-06-29) |
Domain Annotation: ECOD Classification ECOD Database Homepage
Chains | Family Name | Domain Identifier | Architecture | Possible Homology | Homology | Topology | Family | Provenance Source (Version) |
---|---|---|---|---|---|---|---|---|
A | NUDIX_1 | e1vk6A2 | A: a+b two layers | X: beta-Grasp | H: Nudix (From Topology) | T: Nudix | F: NUDIX_1 | ECOD (1.6) |
A | nudC_1st | e1vk6A1 | A: a+b two layers | X: beta-Grasp | H: Nudix (From Topology) | T: Nudix | F: nudC_1st | ECOD (1.6) |
A | nudC_2nd | e1vk6A3 | A: few secondary structure elements | X: Rubredoxin-like | H: Rubredoxin-related | T: Rubredoxin-related | F: nudC_2nd | ECOD (1.6) |
Domain Annotation: CATH CATH Database Homepage
Chain | Domain | Class | Architecture | Topology | Homology | Provenance Source (Version) |
---|---|---|---|---|---|---|
A | 3.90.79.20 | Alpha Beta | Alpha-Beta Complex | Nucleoside Triphosphate Pyrophosphohydrolase | CATH (4.3.0) | |
A | 3.90.79.10 | Alpha Beta | Alpha-Beta Complex | Nucleoside Triphosphate Pyrophosphohydrolase | Nucleoside Triphosphate Pyrophosphohydrolase | CATH (4.3.0) |
Protein Family Annotation Pfam Database Homepage
Chains | Accession | Name | Description | Comments | Source |
---|---|---|---|---|---|
PF09297 | NADH pyrophosphatase zinc ribbon domain (zf-NADH-PPase) | NADH pyrophosphatase zinc ribbon domain | This domain is found in between two duplicated NUDIX domains. It has a zinc ribbon structure. | Domain | |
PF00293 | NUDIX domain (NUDIX) | NUDIX domain | - | Domain |
Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage
InterPro: Protein Family Classification InterPro Database Homepage
Chains | Accession | Name | Type |
---|---|---|---|
IPR022925 | NAD-capped RNA hydrolase NudC | Family | |
IPR050241 | NAD-capped RNA hydrolase NudC subfamily | Family | |
IPR049734 | NADH pyrophosphatase-like, Nudix hydrolase C-terminal domain | Domain | |
IPR000086 | NUDIX hydrolase domain | Domain | |
IPR015376 | Zinc ribbon, NADH pyrophosphatase | Domain | |
IPR015797 | NUDIX hydrolase-like domain superfamily | Homologous Superfamily | |
IPR020084 | NUDIX hydrolase, conserved site | Conserved Site |