MolNFT v1 · #27254 · protein
Crystal structure of a GFO/IDH/MOCA family oxidoreductase from vibrio cholerae
1XEA · Oxidoreductase, GFO/IDH/MOCA family: “Crystal structure of a GFO/IDH/MOCA family oxidoreductase from vibrio cholerae”. X-ray diffraction, 1 ligand (NI), 10 pockets (best druggability 0.87). MolNFT v1 #27254 on GenesisL1: 3D…
- PDB
- 1XEA
- Type
- protein
- Length
- 1,244 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxidoreductase, GFO/IDH/MOCA family
- UniProt
- Q9KKQ4
- Ligands
- NI
- Pockets
- 10 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Oxidoreductase, GFO/IDH/MOCA family | protein | 311 | 41% helix, 28% strand | Q9KKQ4 |
Ligands and binding sites
- NI · Nickel (II) ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 617 | 0.87 | 0.92 | 95 | empty |
| 2 | 287 | 0.78 | 0.90 | 38 | empty |
| 3 | 281 | 0.78 | 0.90 | 37 | empty |
| 4 | 71 | 0.73 | 0.98 | 20 | empty |
| 5 | 70 | 0.72 | 0.97 | 17 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1599 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 1590 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 922 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 880 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 198 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 28 modified (engineered).
Compared structures
- 1XEA · Crystal structure of a Gfo/Idh/MocA family oxidoreductase from Vibrio cholerae · 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 Q9KKQ4
- Elsewhere: RCSB PDB 1XEA · PDBe 1XEA · UniProt Q9KKQ4
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