MolNFT v1 · #12674 · protein
Crystal structure of gluconate kinase
1KO5: “Crystal structure of gluconate kinase”. X-ray diffraction, 2 ligands (ATP, MG), 5 pockets (best druggability 0.59). MolNFT v1 #12674 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1KO5
- Type
- protein
- Length
- 344 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gluconate kinase
- EC
- 2.7.1.12
- UniProt
- P46859
- Ligands
- ATP, MG
- Pockets
- 5 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Gluconate kinase (EC 2.7.1.12) | protein | 172 | 49% helix, 16% strand | P46859 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 315 | 0.59 | 0.78 | 31 | empty |
| 2 | 336 | 0.56 | 0.75 | 44 | MG, ATP |
| 3 | 314 | 0.55 | 0.75 | 35 | MG |
| 4 | 90 | 0.41 | 0.78 | 20 | empty |
| 5 | 50 | 0.30 | 0.76 | 14 | ATP |
Interfaces
1 interface between chains.
- A–B · 1020 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
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 P46859
- Elsewhere: RCSB PDB 1KO5 · PDBe 1KO5 · UniProt P46859
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