MolNFT v1 · #79534 · protein
Crystal structure of a gluconokinase from sinorhizobium meliloti 1021
3T61: “Crystal structure of a gluconokinase from sinorhizobium meliloti 1021”. X-ray diffraction, 1 ligand (PO4), 2 pockets (best druggability 0.71). MolNFT v1 #79534 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3T61
- Type
- protein
- Length
- 351 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gluconokinase
- EC
- 2.7.1.12
- UniProt
- Q92VK3
- Ligands
- PO4
- Pockets
- 2 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gluconokinase (EC 2.7.1.12) | protein | 176 | 53% helix, 12% strand | Q92VK3 |
| B | Gluconokinase (EC 2.7.1.12) | protein | 175 | 53% helix, 13% strand | Q92VK3 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 219 | 0.71 | 0.88 | 54 | PO4 |
| 2 | 181 | 0.71 | 0.89 | 42 | PO4 |
Interfaces
1 interface between chains.
- A–B · 1113 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 modified (engineered).
Compared structures
- 3T61 · Crystal Structure of a gluconokinase from Sinorhizobium meliloti 1021 · the same entry in another collection · chain A against A, TM-score 1.00
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 Q92VK3
- Elsewhere: RCSB PDB 3T61 · PDBe 3T61 · UniProt Q92VK3
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