Research workbench
Crystal structure of E. COLI guanosine kinase in complex with ppgpp
Analyse Crystal structure of E. COLI guanosine kinase in complex with ppgpp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VWP
- Type
- protein
- Length
- 3,390 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inosine-guanosine kinase
- EC
- 2.7.1.73
- UniProt
- P0AEW6
- Ligands
- GMP, G4P, K, MG
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 7 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Inosine-guanosine kinase (EC 2.7.1.73) | protein | 435 | 37% helix, 20% strand | P0AEW6 |
| B | Inosine-guanosine kinase (EC 2.7.1.73) | protein | 428 | 38% helix, 21% strand | P0AEW6 |
| C | Inosine-guanosine kinase (EC 2.7.1.73) | protein | 429 | 38% helix, 20% strand | P0AEW6 |
| E | Inosine-guanosine kinase (EC 2.7.1.73) | protein | 422 | 37% helix, 20% strand | P0AEW6 |
| F | Inosine-guanosine kinase (EC 2.7.1.73) | protein | 412 | 38% helix, 21% strand | P0AEW6 |
| G | Inosine-guanosine kinase (EC 2.7.1.73) | protein | 421 | 37% helix, 20% strand | P0AEW6 |
| H | Inosine-guanosine kinase (EC 2.7.1.73) | protein | 408 | 39% helix, 20% strand | P0AEW6 |
Ligands and binding sites
- GMP · Guanosine · ligand · 16 copies · chains A, B, C, D, E, F, G, H
- G4P · Guanosine-5',3'-tetraphosphate · ligand · 8 copies · chains A, B, C, D, E, F, H, G
- K · Potassium ion · metal · 12 copies · chains A, B, C, D, E, F, G, H
- MG · Magnesium ion · metal · 7 copies · chains A, C, D, E, F, G, H
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 | 375 | 0.79 | 0.89 | 68 | GMP, MG |
| 2 | 1136 | 0.79 | 0.81 | 106 | G4P |
| 3 | 1008 | 0.79 | 0.81 | 109 | G4P |
| 4 | 836 | 0.79 | 0.82 | 94 | G4P |
| 5 | 1027 | 0.79 | 0.80 | 98 | empty |
Interfaces
19 interfaces between chains.
- A–B · 2741 Ų buried · 47 hydrogen bonds · protein-protein
- C–D · 2698 Ų buried · 42 hydrogen bonds · protein-protein
- G–H · 2665 Ų buried · 49 hydrogen bonds · protein-protein
- E–F · 2616 Ų buried · 48 hydrogen bonds · protein-protein
- C–F · 619 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6VWP · Crystal structure of E. coli guanosine kinase in complex with ppGpp · the same entry in another collection · chain H against H, TM-score 1.00
- P0AEW6 · AlphaFold monomer V2.0 prediction for inosine-guanosine kinase (P0AEW6) · a predicted model of the same protein · chain H against A, TM-score 0.90
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 P0AEW6
- Elsewhere: RCSB PDB 6VWP · PDBe 6VWP · UniProt P0AEW6
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