MolNFT v1 · #12684 · protein
Crystal structure of gluconate kinase
1KOF: “Crystal structure of gluconate kinase”. X-ray diffraction, 2 ligands (ACP, MG), 3 pockets (best druggability 0.69). MolNFT v1 #12684 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1KOF
- Type
- protein
- Length
- 342 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
- ACP, MG
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Gluconate kinase (EC 2.7.1.12) | protein | 171 | 46% helix, 16% strand | P46859 |
Ligands and binding sites
- ACP · Phosphomethylphosphonic acid adenylate ester · 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
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 734 | 0.69 | 0.76 | 68 | MG, ACP |
| 2 | 389 | 0.58 | 0.75 | 47 | MG, ACP |
| 3 | 111 | 0.46 | 0.79 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1067 Ų buried · 6 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 1KOF · PDBe 1KOF · UniProt P46859
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