MolNFT v1 · #140563 · protein
The structure of sac-kari protein
5YEQ · Ketol-acid reductoisomerase (NADP(+)): “The structure of sac-kari protein”. X-ray diffraction, 2 ligands (MG, SO4), 6 pockets (best druggability 0.75). MolNFT v1 #140563 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5YEQ
- Type
- protein
- Length
- 658 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ketol-acid reductoisomerase (NADP(+))
- EC
- 1.1.1.86
- UniProt
- A0A0U3H6N8
- Ligands
- MG, SO4
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 61% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ketol-acid reductoisomerase (NADP(+)) (EC 1.1.1.86) | protein | 329 | 61% helix, 12% strand | A0A0U3H6N8 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 7 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 539 | 0.75 | 0.82 | 51 | SO4, MG |
| 2 | 508 | 0.74 | 0.82 | 58 | SO4, MG |
| 3 | 93 | 0.50 | 0.82 | 16 | empty |
| 4 | 90 | 0.45 | 0.80 | 20 | empty |
| 5 | 97 | 0.42 | 0.78 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 6143 Ų buried · 63 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 modified (engineered).
Compared structures
- 5YEQ · The structure of Sac-KARI protein · the same entry in another collection · chain A against A, 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 A0A0U3H6N8
- Elsewhere: RCSB PDB 5YEQ · PDBe 5YEQ · UniProt A0A0U3H6N8
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