Research workbench
Crystal structure of NADPH bound carbonyl reductase from aeropyrum pernix
Analyse Crystal structure of NADPH bound carbonyl reductase from aeropyrum pernix in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5B1Y
- Type
- protein
- Length
- 477 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-oxoacyl-[acyl-carrier-protein] reductase
- EC
- 1.1.1.100
- UniProt
- Q9Y8Y1
- Ligands
- NDP
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) | protein | 234 | 47% helix, 16% strand | Q9Y8Y1 |
| B | 3-oxoacyl-[acyl-carrier-protein] reductase (EC 1.1.1.100) | protein | 243 | 47% helix, 16% strand | Q9Y8Y1 |
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
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 612 | 0.75 | 0.82 | 62 | NDP |
| 2 | 563 | 0.72 | 0.80 | 51 | NDP |
| 3 | 87 | 0.44 | 0.80 | 14 | empty |
| 4 | 124 | 0.43 | 0.77 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1706 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 5B1Y · Crystal structure of NADPH bound carbonyl reductase from Aeropyrum pernix · 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 Q9Y8Y1
- Elsewhere: RCSB PDB 5B1Y · PDBe 5B1Y · UniProt Q9Y8Y1
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