Research workbench
Actinorhodin polyketide ketoreductase mutant P94L bound to NADPH and the inhibitor emodin
Analyse Actinorhodin polyketide ketoreductase mutant P94L bound to NADPH and the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RI3
- Type
- protein
- Length
- 513 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
- EMO, NDP
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Ketoacyl reductase (EC 1.3.1.-) | protein | 257 | 46% helix, 16% strand | P16544 |
| A | Ketoacyl reductase (EC 1.3.1.-) | protein | 256 | 51% helix, 16% strand | P16544 |
Ligands and binding sites
- EMO · 3-methyl-1,6,8-trihydroxyanthraquinone · ligand · 4 copies · chains B, A
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains B, A
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 | 661 | 0.73 | 0.80 | 52 | NDP, EMO |
| 2 | 633 | 0.73 | 0.80 | 57 | NDP, EMO |
| 3 | 61 | 0.41 | 0.81 | 17 | empty |
Interfaces
1 interface between chains.
- B–A · 1642 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 3RI3 · Actinorhodin Polyketide Ketoreductase Mutant P94L bound to NADPH and the Inhibitor Emodin · the same entry in another collection · chain B against B, TM-score 1.00
- P16544 · AlphaFold monomer V2.0 prediction for putative ketoacyl reductase (P16544) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 3RI3 · PDBe 3RI3 · UniProt P16544
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