MolNFT v1 · #153392 · protein
Cryo-EM structure of sulfolobus solfataricus ketol-acid reductoisomerase (sso-kari) in complex with MG2+, NADPH, and cpd at PH7.5
6JCZ · Putative ketol-acid reductoisomerase 2: “Cryo-EM structure of sulfolobus solfataricus ketol-acid reductoisomerase (sso-kari) in complex with MG2+…”. Electron microscopy, 3 ligands (NDP, 9TY, MG), 20 pockets (best druggability 0.85).…
- PDB
- 6JCZ
- Type
- protein
- Length
- 3,959 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative ketol-acid reductoisomerase 2
- EC
- 1.1.1.86
- UniProt
- Q97YJ9
- Ligands
- NDP, 9TY, MG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 4 distinct chains · 47% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, F, I, J, K, L | Putative ketol-acid reductoisomerase 2 (EC 1.1.1.86) | protein | 330 | 49% helix, 10% strand | Q97YJ9 |
| C | Putative ketol-acid reductoisomerase 2 (EC 1.1.1.86) | protein | 331 | 46% helix, 10% strand | Q97YJ9 |
| E, H | Putative ketol-acid reductoisomerase 2 (EC 1.1.1.86) | protein | 329 | 47% helix, 11% strand | Q97YJ9 |
| G | Putative ketol-acid reductoisomerase 2 (EC 1.1.1.86) | protein | 330 | 47% helix, 10% strand | Q97YJ9 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- 9TY · cyclopropane-1,1-dicarboxylic acid · ligand · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
- MG · Magnesium ion · metal · 24 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1114 | 0.85 | 0.86 | 100 | MG, NDP, 9TY |
| 2 | 836 | 0.81 | 0.83 | 76 | MG, 9TY, NDP |
| 3 | 835 | 0.80 | 0.83 | 73 | MG, NDP, 9TY |
| 4 | 842 | 0.80 | 0.83 | 77 | MG, NDP, 9TY |
| 5 | 792 | 0.79 | 0.82 | 70 | NDP, 9TY, MG |
Interfaces
30 interfaces between chains.
- C–D · 5948 Ų buried · 39 hydrogen bonds · protein-protein
- G–H · 5922 Ų buried · 41 hydrogen bonds · protein-protein
- I–J · 5840 Ų buried · 38 hydrogen bonds · protein-protein
- K–L · 5823 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 5819 Ų buried · 41 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6JCZ · Cryo-EM Structure of Sulfolobus solfataricus ketol-acid reductoisomerase (Sso-KARI) in… · the same entry in another collection · chain L against L, 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 Q97YJ9
- Elsewhere: RCSB PDB 6JCZ · PDBe 6JCZ · UniProt Q97YJ9
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