MolNFT v1 · #154877 · protein
277 K cryoem structure of sso-kari in complex with MG2+, NADH and cpd
6KPA · Ketol-acid reductoisomerase: “277 K cryoem structure of sso-kari in complex with MG2+, NADH and cpd”. Electron microscopy, 3 ligands (NAI, 9TY, MG), 20 pockets (best druggability 0.84). MolNFT v1 #154877 on GenesisL1: 3D structure…
- PDB
- 6KPA
- Type
- protein
- Length
- 3,936 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ketol-acid reductoisomerase
- UniProt
- A0A157T175
- Ligands
- NAI, 9TY, MG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 1 distinct chain · 56% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H, I, J, K, L | Ketol-acid reductoisomerase | protein | 328 | 56% helix, 12% strand | A0A157T175 |
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 · 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1174 | 0.84 | 0.85 | 140 | NAI, 9TY, MG |
| 2 | 1165 | 0.84 | 0.85 | 129 | NAI, 9TY, MG |
| 3 | 1141 | 0.84 | 0.85 | 131 | NAI, 9TY, MG |
| 4 | 785 | 0.81 | 0.84 | 90 | NAI, 9TY, MG |
| 5 | 943 | 0.80 | 0.81 | 98 | MG, NAI, 9TY |
Interfaces
30 interfaces between chains.
- C–D · 5529 Ų buried · 37 hydrogen bonds · protein-protein
- E–F · 5525 Ų buried · 36 hydrogen bonds · protein-protein
- G–H · 5520 Ų buried · 37 hydrogen bonds · protein-protein
- K–L · 5520 Ų buried · 38 hydrogen bonds · protein-protein
- I–J · 5507 Ų buried · 37 hydrogen bonds · protein-protein
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 A0A157T175
- Elsewhere: RCSB PDB 6KPA · PDBe 6KPA · UniProt A0A157T175
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