Research workbench
Crystal structure of the chloroplastic gamma-ketol reductase from arabidopsis thaliana bound to 13KOTE and NADP
Analyse Crystal structure of the chloroplastic gamma-ketol reductase from arabidopsis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5A4D
- Type
- protein
- Length
- 2,597 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative quinone-oxidoreductase homolog, chloroplastic
- EC
- 1.-.-.-
- UniProt
- Q9SV68
- Ligands
- NAP, KZH
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, F, G | Putative quinone-oxidoreductase homolog, chloroplastic (EC 1.-.-.-) | protein | 327 | 31% helix, 29% strand | Q9SV68 |
| B | Putative quinone-oxidoreductase homolog, chloroplastic (EC 1.-.-.-) | protein | 324 | 30% helix, 28% strand | Q9SV68 |
| C, H | Putative quinone-oxidoreductase homolog, chloroplastic (EC 1.-.-.-) | protein | 326 | 29% helix, 29% strand | Q9SV68 |
| E | Putative quinone-oxidoreductase homolog, chloroplastic (EC 1.-.-.-) | protein | 313 | 31% helix, 28% strand | Q9SV68 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- KZH · (13-oxo-9(Z),11(E),15(Z)-octadecatrienoic acid) · ligand · 6 copies · chains A, C, D, B, F, G, H, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 842 | 0.81 | 0.83 | 87 | NAP, KZH |
| 2 | 732 | 0.80 | 0.84 | 81 | NAP, KZH |
| 3 | 708 | 0.80 | 0.84 | 79 | NAP, KZH |
| 4 | 727 | 0.80 | 0.84 | 73 | KZH, NAP |
| 5 | 621 | 0.79 | 0.84 | 65 | NAP |
Interfaces
16 interfaces between chains.
- F–H · 531 Ų buried · 1 hydrogen bond · protein-protein
- E–G · 527 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 488 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 464 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 438 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5A4D · Crystal structure of the chloroplastic gamma-ketol reductase from Arabidopsis thaliana… · the same entry in another collection · chain H against H, TM-score 1.00
- Q9SV68 · AlphaFold monomer V2.0 prediction for chloroplast envelope quinone oxidoreductase homolog… · a predicted model of the same protein · chain B against A, TM-score 0.99
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 5A4D · PDBe 5A4D · UniProt Q9SV68
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