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Substrate-bound structure of a ketoreductase from the second module of the amphotericin polyketide synthases
Analyse Substrate-bound structure of a ketoreductase from the second module of the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XWV
- Type
- protein
- Length
- 954 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Amphb
- UniProt
- Q93NW7
- Ligands
- NDP, 8H6
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Amphb | protein | 477 | 43% helix, 20% strand | Q93NW7 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- 8H6 · S-[2-[3-[[(2R)-3,3-dimethyl-2,4-bis(oxidanyl) butanoyl]amino]propanoylamino]ethyl] (2R)-2-methyl-3-oxidanylidene-pentanethioate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 571 | 0.79 | 0.85 | 70 | NDP, 8H6 |
| 2 | 631 | 0.78 | 0.83 | 83 | NDP, 8H6 |
| 3 | 936 | 0.78 | 0.80 | 113 | empty |
| 4 | 359 | 0.66 | 0.80 | 47 | empty |
| 5 | 70 | 0.29 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 527 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5XWV · Substrate-bound Structure of a Ketoreductase from the Second Module of the amphotericin… · 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 Q93NW7
- Elsewhere: RCSB PDB 5XWV · PDBe 5XWV · UniProt Q93NW7
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