Research workbench
Crystal structure of oligomeric E.COLI guanylate kinase in complex with GDP
Analyse Crystal structure of oligomeric E.COLI guanylate kinase in complex with GDP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2AN9
- Type
- protein
- Length
- 410 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanylate kinase
- EC
- 2.7.4.8
- UniProt
- P60546
- Ligands
- GDP, GMP, K
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Guanylate kinase (EC 2.7.4.8) | protein | 205 | 47% helix, 21% strand | P60546 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- GMP · Guanosine · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 465 | 0.70 | 0.81 | 47 | K, GDP |
| 2 | 433 | 0.68 | 0.80 | 39 | K, GDP |
| 3 | 169 | 0.44 | 0.75 | 31 | empty |
| 4 | 117 | 0.36 | 0.73 | 17 | empty |
| 5 | 67 | 0.34 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1649 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 2AN9 · Crystal Structure Of Oligomeric E.coli Guanylate Kinase In Complex With GDP · the same entry in another collection · chain A against A, TM-score 1.00
- P60546 · AlphaFold monomer V2.0 prediction for guanylate kinase (P60546) · a predicted model of the same protein · chain A 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 P60546
- Elsewhere: RCSB PDB 2AN9 · PDBe 2AN9 · UniProt P60546
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