MolNFT v1 · #113042 · protein
Crystal structure of the chloroplastic gamma-ketol reductase from arabidopsis thaliana bound to 13-oxo-9(Z),11(E),15(Z)- octadecatrienoic acid.
5A3J · Putative quinone-oxidoreductase homolog, chloroplastic: “Crystal structure of the chloroplastic gamma-ketol reductase from arabidopsis thaliana bound to…”. X-ray diffraction, 1 ligand (KZH), 20 pockets (best druggability 0.87).…
- PDB
- 5A3J
- Type
- protein
- Length
- 3,913 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative quinone-oxidoreductase homolog, chloroplastic
- EC
- 1.-.-.-
- UniProt
- Q9SV68
- Ligands
- KZH
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Putative quinone-oxidoreductase homolog, chloroplastic (EC 1.-.-.-) | protein | 326 | 30% helix, 29% strand | Q9SV68 |
| B, G, I | Putative quinone-oxidoreductase homolog, chloroplastic (EC 1.-.-.-) | protein | 325 | 29% helix, 28% strand | Q9SV68 |
| C, E, F, H, J, L | Putative quinone-oxidoreductase homolog, chloroplastic (EC 1.-.-.-) | protein | 327 | 30% helix, 29% strand | Q9SV68 |
| K | Putative quinone-oxidoreductase homolog, chloroplastic (EC 1.-.-.-) | protein | 324 | 30% helix, 27% strand | Q9SV68 |
Ligands and binding sites
- KZH · (13-oxo-9(Z),11(E),15(Z)-octadecatrienoic acid) · ligand · 12 copies · chains A, B, D, C, E, F, H, G, 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1097 | 0.87 | 0.87 | 149 | KZH |
| 2 | 811 | 0.82 | 0.85 | 100 | KZH |
| 3 | 544 | 0.82 | 0.87 | 68 | KZH |
| 4 | 713 | 0.82 | 0.85 | 89 | KZH |
| 5 | 704 | 0.82 | 0.85 | 78 | KZH |
Interfaces
23 interfaces between chains.
- I–L · 504 Ų buried · 0 hydrogen bonds · protein-protein
- F–H · 496 Ų buried · 0 hydrogen bonds · protein-protein
- E–G · 492 Ų buried · 0 hydrogen bonds · protein-protein
- J–K · 491 Ų buried · 0 hydrogen bonds · protein-protein
- J–L · 481 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5A3J · Crystal structure of the chloroplastic gamma-ketol reductase from Arabidopsis thaliana… · 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 Q9SV68
- Elsewhere: RCSB PDB 5A3J · PDBe 5A3J · UniProt Q9SV68
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