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
- 5TII
- Type
- protein
- Length
- 1,915 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
- 16 · best druggability 0.85
Structure
x-ray diffraction · 8 distinct chains · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-oxoacyl-acp reductase | protein | 241 | 49% helix, 17% strand | A0A023PKG5 |
| D | 3-oxoacyl-acp reductase | protein | 244 | 45% helix, 16% strand | A0A023PKG5 |
| E | 3-oxoacyl-acp reductase | protein | 238 | 49% helix, 17% strand | A0A023PKG5 |
| G | 3-oxoacyl-acp reductase | protein | 232 | 48% helix, 16% strand | A0A023PKG5 |
| H | 3-oxoacyl-acp reductase | protein | 233 | 46% helix, 17% strand | A0A023PKG5 |
| B | 3-oxoacyl-acp reductase | protein | 241 | 49% helix, 17% strand | A0A023PKG5 |
| C | 3-oxoacyl-acp reductase | protein | 236 | 49% helix, 17% strand | A0A023PKG5 |
| F | 3-oxoacyl-acp reductase | protein | 250 | 50% helix, 16% strand | A0A023PKG5 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 3 copies · chains E, B, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 974 | 0.85 | 0.86 | 70 | empty |
| 2 | 997 | 0.85 | 0.86 | 69 | empty |
| 3 | 1045 | 0.76 | 0.78 | 103 | NDP |
| 4 | 536 | 0.75 | 0.82 | 57 | empty |
| 5 | 1152 | 0.75 | 0.77 | 102 | empty |
Interfaces
13 interfaces between chains.
- G–H · 1917 Ų buried · 34 hydrogen bonds · protein-protein
- D–E · 1850 Ų buried · 29 hydrogen bonds · protein-protein
- A–C · 1850 Ų buried · 29 hydrogen bonds · protein-protein
- B–F · 1740 Ų buried · 36 hydrogen bonds · protein-protein
- A–F · 1593 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 5TII · Comprehensive Analysis of a Novel Ketoreductase for Pentangular Polyphenol Biosynthesis · 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 A0A023PKG5
- Elsewhere: RCSB PDB 5TII · PDBe 5TII · UniProt A0A023PKG5
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