Research workbench
Structure of E. COLI dgtpase bound to T7 bacteriophage protein GP1.2 and dgtp
Analyse Structure of E. COLI dgtpase bound to T7 bacteriophage protein GP1.2 and dgtp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7U66
- Type
- protein
- Length
- 3,348 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Deoxyguanosinetriphosphate triphosphohydrolase; Inhibitor of dgtpase
- EC
- 3.1.5.1
- UniProt
- P15723, P03780
- Ligands
- DGT, MG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 2 distinct chains · 58% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Deoxyguanosinetriphosphate triphosphohydrolase (EC 3.1.5.1) | protein | 474 | 61% helix, 1% strand | P15723 |
| G, H, I, J, K, L | Inhibitor of dgtpase | protein | 84 | 40% helix, 32% strand | P03780 |
Ligands and binding sites
- DGT · 2'-deoxyguanosine-5'-triphosphate · ligand · 6 copies · chains A, G, H, B, I, C, J, D, K, E, L, F
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, 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 | 1071 | 0.85 | 0.86 | 99 | DGT |
| 2 | 763 | 0.85 | 0.88 | 76 | DGT |
| 3 | 1084 | 0.85 | 0.86 | 104 | DGT, MG |
| 4 | 1170 | 0.85 | 0.86 | 101 | DGT, MG |
| 5 | 1105 | 0.85 | 0.86 | 98 | MG, DGT |
Interfaces
21 interfaces between chains.
- A–B · 1797 Ų buried · 16 hydrogen bonds · protein-protein
- E–F · 1793 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 1792 Ų buried · 16 hydrogen bonds · protein-protein
- J–D · 736 Ų buried · 6 hydrogen bonds · protein-protein
- I–C · 735 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 7U66 · Structure of E. coli dGTPase bound to T7 bacteriophage protein Gp1.2 and dGTP · the same entry in another collection · chain F against F, TM-score 1.00
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
- Every structure of UniProt P03780
- Elsewhere: RCSB PDB 7U66 · PDBe 7U66 · UniProt P15723 · UniProt P03780
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