Research workbench
Mutant slackia exigua kari ddv in complex with NAD and an inhibitor
Analyse Mutant slackia exigua kari ddv in complex with NAD and an inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KQX
- Type
- protein
- Length
- 657 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ketol-acid reductoisomerase
- EC
- 1.1.1.86
- UniProt
- D0WGK0
- Ligands
- NAD, HIO, HIS, MG
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 61% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ketol-acid reductoisomerase (EC 1.1.1.86) | protein | 322 | 62% helix, 13% strand | D0WGK0 |
| B | Ketol-acid reductoisomerase (EC 1.1.1.86) | protein | 335 | 60% helix, 12% strand | D0WGK0 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- HIO · N-hydroxy-N-isopropyloxamic acid · ligand · 2 copies · chains A, B
- HIS · Histidine · ligand · chains B
- MG · Magnesium ion · metal · 10 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 | 398 | 0.76 | 0.86 | 52 | NAD, MG, HIO |
| 2 | 385 | 0.76 | 0.86 | 55 | HIO, MG, NAD |
| 3 | 140 | 0.40 | 0.74 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 6152 Ų buried · 70 hydrogen bonds · protein-protein
Compared structures
- 4KQX · Mutant Slackia exigua KARI DDV in complex with NAD and an inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- D0WGK0 · AlphaFold monomer V2.0 prediction for ketol-acid reductoisomerase (NADP(+)) (D0WGK0) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 D0WGK0
- Elsewhere: RCSB PDB 4KQX · PDBe 4KQX · UniProt D0WGK0
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