MolNFT v1 · #7911 · protein
Refined structure of the complex between guanylate kinase and its substrate gmp at 2.0 ångströms resolution
1GKY: “Refined structure of the complex between guanylate kinase and its substrate gmp at 2.0 ångströms resolution”. X-ray diffraction, 3 ligands (ACE, 5GP, SO4), 1 pocket (best druggability 0.69). MolNFT v1 #7911 on GenesisL1: 3D…
- PDB
- 1GKY
- Type
- protein
- Length
- 186 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanylate kinase
- EC
- 2.7.4.8
- UniProt
- P15454
- Ligands
- ACE, 5GP, SO4
- Pockets
- 1 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanylate kinase (EC 2.7.4.8) | protein | 186 | 45% helix, 23% strand | P15454 |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains A
- 5GP · Guanosine-5'-monophosphate · ligand · chains A
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 570 | 0.69 | 0.78 | 47 | SO4, 5GP |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 1GKY · Refined structure of the complex between guanylate kinase and its substrate gmp at 2.0… · the same entry in another collection · chain A against A, TM-score 1.00
- P15454 · AlphaFold monomer V2.0 prediction for guanylate kinase (P15454) · a predicted model of the same protein · chain A against A, TM-score 0.81
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 P15454
- Elsewhere: RCSB PDB 1GKY · PDBe 1GKY · UniProt P15454
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