Research workbench
Crystal structure of a short chain dehydrogenase from burkholderia cenocepacia J2315 in complex with NAD
Analyse Crystal structure of a short chain dehydrogenase from burkholderia cenocepacia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5U8P
- Type
- protein
- Length
- 584 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Short chain dehydrogenase
- UniProt
- B4EEE3
- Ligands
- NAD, MG
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Short chain dehydrogenase | protein | 292 | 43% helix, 13% strand | B4EEE3 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 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 | 448 | 0.79 | 0.87 | 58 | NAD |
| 2 | 446 | 0.79 | 0.87 | 55 | NAD |
| 3 | 110 | 0.41 | 0.77 | 21 | empty |
| 4 | 103 | 0.38 | 0.75 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 2273 Ų buried · 39 hydrogen bonds · protein-protein
Compared structures
- 5U8P · Crystal structure of a short chain dehydrogenase from Burkholderia cenocepacia J2315 in… · 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 B4EEE3
- Elsewhere: RCSB PDB 5U8P · PDBe 5U8P · UniProt B4EEE3
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