MolNFT v1 · #138460 · protein
Crystal structure of oxidoreductase (short chain DEHYDROGENASE/REDUCTASE family) from burkholderia thailandensis complexed with NADH
5WJS · Oxidoreductase, short chain DEHYDROGENASE/REDUCTASE family: “Crystal structure of oxidoreductase (short chain DEHYDROGENASE/REDUCTASE family) from burkholderia…”. X-ray diffraction, 1 ligand (NAI), 7 pockets (best druggability…
- PDB
- 5WJS
- Type
- protein
- Length
- 516 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxidoreductase, short chain DEHYDROGENASE/REDUCTASE family
- UniProt
- Q2SZC0
- Ligands
- NAI
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Oxidoreductase, short chain DEHYDROGENASE/REDUCTASE family | protein | 258 | 50% helix, 15% strand | Q2SZC0 |
Ligands and binding sites
- NAI · 1,4-dihydronicotinamide adenine dinucleotide · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 16 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 486 | 0.74 | 0.83 | 40 | NAI, EDO |
| 2 | 462 | 0.74 | 0.83 | 44 | NAI, EDO |
| 3 | 149 | 0.48 | 0.78 | 33 | EDO |
| 4 | 128 | 0.43 | 0.76 | 24 | empty |
| 5 | 115 | 0.38 | 0.75 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 1739 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 5WJS · Crystal structure of oxidoreductase (short chain dehydrogenase/reductase family) from… · 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 Q2SZC0
- Elsewhere: RCSB PDB 5WJS · PDBe 5WJS · UniProt Q2SZC0
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