Research workbench
Crystal structure of F189W actinorhodin polyketide ketoreductase with NADPH
Analyse Crystal structure of F189W actinorhodin polyketide ketoreductase with NADPH in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DC0
- Type
- protein
- Length
- 519 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ketoacyl reductase
- EC
- 1.3.1.-
- UniProt
- P16544
- Ligands
- NDP
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ketoacyl reductase (EC 1.3.1.-) | protein | 258 | 50% helix, 16% strand | P16544 |
| B | Ketoacyl reductase (EC 1.3.1.-) | protein | 261 | 44% helix, 15% strand | P16544 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 590 | 0.79 | 0.84 | 65 | NDP |
| 2 | 689 | 0.74 | 0.80 | 54 | NDP |
| 3 | 90 | 0.43 | 0.79 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1594 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 4DC0 · Crystal Structure of F189W Actinorhodin Polyketide Ketoreductase with NADPH · the same entry in another collection · chain A against A, TM-score 1.00
- P16544 · AlphaFold monomer V2.0 prediction for putative ketoacyl reductase (P16544) · 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 P16544
- Elsewhere: RCSB PDB 4DC0 · PDBe 4DC0 · UniProt P16544
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