MolNFT v1 · #159242 · protein
Structure of escherichia COLI dgtpase bound to dgtp-1-thiol
6OIW · Deoxyguanosinetriphosphate triphosphohydrolase: “Structure of escherichia COLI dgtpase bound to dgtp-1-thiol”. X-ray diffraction, 3 ligands (T8T, MN, MG), 20 pockets (best druggability 0.82). MolNFT v1 #159242 on GenesisL1: 3D…
- PDB
- 6OIW
- Type
- protein
- Length
- 3,020 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
- T8T, MN, MG
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 60% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Deoxyguanosinetriphosphate triphosphohydrolase (EC 3.1.5.1) | protein | 504 | 61% helix, 2% strand | P15723 |
| B, C, E, F | Deoxyguanosinetriphosphate triphosphohydrolase (EC 3.1.5.1) | protein | 503 | 60% helix, 2% strand | P15723 |
Ligands and binding sites
- T8T · 2'-deoxyguanosine-5'-O-(1-thiotriphosphate) · ligand · 6 copies · chains A, B, C, D, F, E
- MN · Manganese (II) ion · metal · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 3 copies · chains A, E, F
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 | 919 | 0.82 | 0.84 | 89 | empty |
| 2 | 1022 | 0.82 | 0.83 | 90 | empty |
| 3 | 1081 | 0.80 | 0.81 | 91 | empty |
| 4 | 719 | 0.77 | 0.81 | 62 | empty |
| 5 | 680 | 0.76 | 0.81 | 62 | empty |
Interfaces
12 interfaces between chains.
- A–F · 2436 Ų buried · 35 hydrogen bonds · protein-protein
- B–D · 2348 Ų buried · 47 hydrogen bonds · protein-protein
- C–E · 2301 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 789 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 756 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 6OIW · Structure of Escherichia coli dGTPase bound to dGTP-1-thiol · 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 B 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 6OIW · PDBe 6OIW · UniProt P15723
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