MolNFT v1 · #153999 · protein
Crystal structure of ketol-acid reductoisomerase from corynebacterium glutamicum
6JX2 · Ketol-acid reductoisomerase (NADP(+)): “Crystal structure of ketol-acid reductoisomerase from corynebacterium glutamicum”. X-ray diffraction, 2 ligands (NAP, MG), 11 pockets (best druggability 0.77). MolNFT v1 #153999 on GenesisL1…
- PDB
- 6JX2
- Type
- protein
- Length
- 1,298 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ketol-acid reductoisomerase (NADP(+))
- EC
- 1.1.1.86
- UniProt
- Q57179
- Ligands
- NAP, MG
- Pockets
- 11 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 60% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ketol-acid reductoisomerase (NADP(+)) (EC 1.1.1.86) | protein | 325 | 61% helix, 12% strand | Q57179 |
| B | Ketol-acid reductoisomerase (NADP(+)) (EC 1.1.1.86) | protein | 327 | 61% helix, 12% strand | Q57179 |
| C | Ketol-acid reductoisomerase (NADP(+)) (EC 1.1.1.86) | protein | 324 | 59% helix, 12% strand | Q57179 |
| D | Ketol-acid reductoisomerase (NADP(+)) (EC 1.1.1.86) | protein | 322 | 61% helix, 12% strand | Q57179 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 3 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 13 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 803 | 0.77 | 0.81 | 73 | MG |
| 2 | 788 | 0.76 | 0.80 | 84 | MG, NAP |
| 3 | 474 | 0.74 | 0.83 | 58 | MG, NAP |
| 4 | 793 | 0.74 | 0.79 | 69 | MG, NAP |
| 5 | 299 | 0.59 | 0.78 | 33 | empty |
Interfaces
4 interfaces between chains.
- A–B · 5538 Ų buried · 58 hydrogen bonds · protein-protein
- C–D · 5352 Ų buried · 55 hydrogen bonds · protein-protein
- B–C · 337 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 329 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6JX2 · Crystal structure of Ketol-acid reductoisomerase from Corynebacterium glutamicum · the same entry in another collection · chain D against D, TM-score 1.00
- Q57179 · AlphaFold monomer V2.0 prediction for ketol-acid reductoisomerase (NADP(+)) (Q57179) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 Q57179
- Elsewhere: RCSB PDB 6JX2 · PDBe 6JX2 · UniProt Q57179
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