Research workbench
Cryo-EM structure of sulfolobus solfataricus ketol-acid reductoisomerase (sso-kari) in complex with MG2+, NADH, and cpd at PH7.5
Analyse Cryo-EM structure of sulfolobus solfataricus ketol-acid reductoisomerase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JD1
- Type
- protein
- Length
- 3,953 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
- NAI, 9TY, MG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 7 distinct chains · 49% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Putative ketol-acid reductoisomerase 2 (EC 1.1.1.86) | protein | 330 | 51% helix, 10% strand | Q97YJ9 |
| B | Putative ketol-acid reductoisomerase 2 (EC 1.1.1.86) | protein | 331 | 48% helix, 11% strand | Q97YJ9 |
| C | Putative ketol-acid reductoisomerase 2 (EC 1.1.1.86) | protein | 331 | 50% helix, 9% strand | Q97YJ9 |
| E, H, J | Putative ketol-acid reductoisomerase 2 (EC 1.1.1.86) | protein | 329 | 47% helix, 11% strand | Q97YJ9 |
| F, G | Putative ketol-acid reductoisomerase 2 (EC 1.1.1.86) | protein | 330 | 52% helix, 10% strand | Q97YJ9 |
| I, L | Putative ketol-acid reductoisomerase 2 (EC 1.1.1.86) | protein | 328 | 48% helix, 11% strand | Q97YJ9 |
| K | Putative ketol-acid reductoisomerase 2 (EC 1.1.1.86) | protein | 328 | 45% helix, 10% strand | Q97YJ9 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · 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 · 36 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 | 1171 | 0.85 | 0.86 | 113 | MG, NAI, 9TY |
| 2 | 991 | 0.82 | 0.83 | 102 | MG, NAI, 9TY |
| 3 | 738 | 0.82 | 0.85 | 80 | MG, NAI, 9TY |
| 4 | 904 | 0.81 | 0.83 | 97 | MG, NAI, 9TY |
| 5 | 744 | 0.81 | 0.84 | 78 | MG, NAI, 9TY |
Interfaces
30 interfaces between chains.
- G–H · 5908 Ų buried · 44 hydrogen bonds · protein-protein
- K–L · 5889 Ų buried · 44 hydrogen bonds · protein-protein
- C–D · 5875 Ų buried · 41 hydrogen bonds · protein-protein
- E–F · 5822 Ų buried · 38 hydrogen bonds · protein-protein
- A–B · 5811 Ų buried · 40 hydrogen bonds · protein-protein
Compared structures
- 6JD1 · 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 6JD1 · PDBe 6JD1 · UniProt Q97YJ9
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