Research workbench
Comprehensive analysis of a novel ketoreductase for pentangular polyphenol biosynthesis
Analyse Comprehensive analysis of a novel ketoreductase for pentangular polyphenol… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5THQ
- Type
- protein
- Length
- 1,996 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-oxoacyl-acp reductase
- UniProt
- A0A023PKG5
- Ligands
- NDP
- Pockets
- 19 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G, A | 3-oxoacyl-acp reductase | protein | 248 | 52% helix, 17% strand | A0A023PKG5 |
| B, C, F, E, H, D | 3-oxoacyl-acp reductase | protein | 250 | 51% helix, 16% strand | A0A023PKG5 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 8 copies · chains G, B, C, F, A, E, H, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 987 | 0.85 | 0.86 | 64 | empty |
| 2 | 1015 | 0.84 | 0.86 | 64 | empty |
| 3 | 660 | 0.79 | 0.83 | 59 | NDP |
| 4 | 537 | 0.78 | 0.85 | 57 | NDP |
| 5 | 645 | 0.78 | 0.83 | 57 | NDP |
Interfaces
14 interfaces between chains.
- E–D · 1835 Ų buried · 34 hydrogen bonds · protein-protein
- C–F · 1760 Ų buried · 33 hydrogen bonds · protein-protein
- G–B · 1727 Ų buried · 31 hydrogen bonds · protein-protein
- A–H · 1722 Ų buried · 31 hydrogen bonds · protein-protein
- E–H · 1603 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 5THQ · Comprehensive Analysis of a Novel Ketoreductase for Pentangular Polyphenol Biosynthesis · the same entry in another collection · chain G against G, 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 A0A023PKG5
- Elsewhere: RCSB PDB 5THQ · PDBe 5THQ · UniProt A0A023PKG5
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