Research workbench
Apo structure of vibrio cholerae dgtpase protein VC1979
Analyse Apo structure of vibrio cholerae dgtpase protein VC1979 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LWZ
- Type
- protein
- Length
- 2,340 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxyguanosinetriphosphate triphosphohydrolase-like protein 1
- UniProt
- Q9KQL9
- Ligands
- NI
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 6 distinct chains · 66% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Deoxyguanosinetriphosphate triphosphohydrolase-like protein 1 | protein | 385 | 66% helix, 3% strand | Q9KQL9 |
| A | Deoxyguanosinetriphosphate triphosphohydrolase-like protein 1 | protein | 400 | 63% helix, 4% strand | Q9KQL9 |
| D | Deoxyguanosinetriphosphate triphosphohydrolase-like protein 1 | protein | 392 | 66% helix, 3% strand | Q9KQL9 |
| C | Deoxyguanosinetriphosphate triphosphohydrolase-like protein 1 | protein | 390 | 67% helix, 4% strand | Q9KQL9 |
| F | Deoxyguanosinetriphosphate triphosphohydrolase-like protein 1 | protein | 373 | 68% helix, 3% strand | Q9KQL9 |
| E | Deoxyguanosinetriphosphate triphosphohydrolase-like protein 1 | protein | 400 | 65% helix, 3% strand | Q9KQL9 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · 6 copies · chains B, A, D, C, F, 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, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1123 | 0.87 | 0.88 | 97 | empty |
| 2 | 1176 | 0.85 | 0.86 | 95 | empty |
| 3 | 1011 | 0.83 | 0.84 | 83 | empty |
| 4 | 625 | 0.80 | 0.85 | 55 | empty |
| 5 | 880 | 0.72 | 0.77 | 65 | NI |
Interfaces
10 interfaces between chains.
- B–A · 1722 Ų buried · 16 hydrogen bonds · protein-protein
- F–E · 1720 Ų buried · 21 hydrogen bonds · protein-protein
- D–C · 1552 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 678 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 626 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 7LWZ · Apo Structure of Vibrio cholerae dGTPase protein VC1979 · the same entry in another collection · chain E against E, TM-score 1.00
- Q9KQL9 · AlphaFold monomer V2.0 prediction for deoxyguanosinetriphosphate triphosphohydrolase-like… · a predicted model of the same protein · chain D 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 Q9KQL9
- Elsewhere: RCSB PDB 7LWZ · PDBe 7LWZ · UniProt Q9KQL9
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