Research workbench
Refined structure of the complex between guanylate kinase and its substrate gmp at 2.0 ångströms resolution
Analyse Refined structure of the complex between guanylate kinase and its substrate gmp… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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