Research workbench
Deoxyguanosinetriphosphate triphosphohydrolase from escherichia COLI with nickel
Analyse Deoxyguanosinetriphosphate triphosphohydrolase from escherichia COLI with nickel in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4XDS
- Type
- protein
- Length
- 2,980 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxyguanosinetriphosphate triphosphohydrolase
- EC
- 3.1.5.1
- UniProt
- P15723
- Ligands
- NI, SO4
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 64% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Deoxyguanosinetriphosphate triphosphohydrolase (EC 3.1.5.1) | protein | 492 | 64% helix, 2% strand | P15723 |
| B | Deoxyguanosinetriphosphate triphosphohydrolase (EC 3.1.5.1) | protein | 494 | 64% helix, 2% strand | P15723 |
| C, E | Deoxyguanosinetriphosphate triphosphohydrolase (EC 3.1.5.1) | protein | 503 | 63% helix, 2% strand | P15723 |
| D, F | Deoxyguanosinetriphosphate triphosphohydrolase (EC 3.1.5.1) | protein | 494 | 64% helix, 2% strand | P15723 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 6 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 79 copies · chains A, B, F, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1045 | 0.80 | 0.81 | 108 | SO4 |
| 2 | 1138 | 0.78 | 0.80 | 110 | SO4 |
| 3 | 1155 | 0.78 | 0.80 | 105 | SO4 |
| 4 | 737 | 0.78 | 0.82 | 93 | SO4 |
| 5 | 719 | 0.75 | 0.80 | 94 | SO4 |
Interfaces
12 interfaces between chains.
- C–D · 2293 Ų buried · 31 hydrogen bonds · protein-protein
- E–F · 2241 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 1889 Ų buried · 30 hydrogen bonds · protein-protein
- A–E · 774 Ų buried · 9 hydrogen bonds · protein-protein
- D–F · 716 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4XDS · Deoxyguanosinetriphosphate Triphosphohydrolase from Escherichia coli with Nickel · the same entry in another collection · chain F against F, TM-score 1.00
- P15723 · AlphaFold monomer V2.0 prediction for deoxyguanosinetriphosphate triphosphohydrolase… · a predicted model of the same protein · chain F against A, TM-score 0.99
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P15723
- Elsewhere: RCSB PDB 4XDS · PDBe 4XDS · UniProt P15723
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