Research workbench
IlvC, a ketol-acid reductoisomerase, from Streptococcus pneumoniae_WT
Analyse IlvC, a ketol-acid reductoisomerase, from Streptococcus pneumoniae_WT in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6L2I
- Type
- protein
- Length
- 647 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.69
- Source
- Streptococcus pneumoniae D39
- Molecule
- Ketol-acid reductoisomerase (NADP(+))
- EC
- 1.1.1.86
- UniProt
- Q04M32
- Ligands
- NAP, MG, SO4
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · resolution 1.69 · 2 distinct chains · 60% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ketol-acid reductoisomerase (NADP(+)) (EC 1.1.1.86) | protein | 324 | 61% helix, 11% strand | Q04M32 |
| B | Ketol-acid reductoisomerase (NADP(+)) (EC 1.1.1.86) | protein | 323 | 60% helix, 12% strand | Q04M32 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 10 copies · chains A, B
- GOL · Glycerol · additive · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 544 | 0.78 | 0.85 | 69 | NAP, MG, SO4 |
| 2 | 547 | 0.76 | 0.83 | 52 | SO4 |
| 3 | 149 | 0.51 | 0.79 | 20 | GOL |
| 4 | 143 | 0.48 | 0.78 | 20 | GOL |
| 5 | 102 | 0.41 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 5528 Ų buried · 52 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6L2I · Ilvc, a ketol-acid reductoisomerase, from streptococcus PNEUMONIAE_WT · the same entry in another collection · chain A against A, TM-score 1.00
- Q04M32 · AlphaFold monomer V2.0 prediction for ketol-acid reductoisomerase (NADP(+)) (Q04M32) · a predicted model of the same protein · chain B 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 Q04M32
- Elsewhere: RCSB PDB 6L2I · PDBe 6L2I · UniProt Q04M32
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