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Crystal structure of a short chain DEHYDROGENASE/REDUCTASE sdr from burkholderia phymatum with partially occupied NAD
Analyse Crystal structure of a short chain DEHYDROGENASE/REDUCTASE sdr from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6D9Y
- Type
- protein
- Length
- 502 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Short-chain DEHYDROGENASE/REDUCTASE sdr
- EC
- 1.3.8.-
- UniProt
- B2JLJ0
- Ligands
- OXM, NAD
- Pockets
- 4 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Short-chain DEHYDROGENASE/REDUCTASE sdr (EC 1.3.8.-) | protein | 251 | 45% helix, 16% strand | B2JLJ0 |
Ligands and binding sites
- OXM · Oxamic acid · ligand · 3 copies · chains A, B
- NAD · Nicotinamide-adenine-dinucleotide · ligand · chains B
- FMT · Formic acid · additive · 5 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 420 | 0.78 | 0.86 | 47 | NAD, OXM |
| 2 | 529 | 0.68 | 0.78 | 43 | EDO |
| 3 | 129 | 0.52 | 0.81 | 21 | empty |
| 4 | 59 | 0.31 | 0.75 | 10 | OXM |
Interfaces
1 interface between chains.
- A–B · 1676 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 6D9Y · Crystal structure of a short chain dehydrogenase/reductase SDR from Burkholderia phymatum… · 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 B2JLJ0
- Elsewhere: RCSB PDB 6D9Y · PDBe 6D9Y · UniProt B2JLJ0
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