Research workbench
Crystal structure of a short chain dehydrogenase from burkholderia cenocepacia J2315 in complex with NADP.
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
- 5U4S
- Type
- protein
- Length
- 467 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative short chain dehydrogenase
- UniProt
- B4EFS5
- Ligands
- NAP, BEZ, PO4
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative short chain dehydrogenase | protein | 230 | 49% helix, 17% strand | B4EFS5 |
| B | Putative short chain dehydrogenase | protein | 237 | 50% helix, 16% strand | B4EFS5 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- BEZ · Benzoic acid · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 446 | 0.77 | 0.86 | 52 | NAP, BEZ |
| 2 | 420 | 0.76 | 0.85 | 43 | NAP, BEZ |
| 3 | 60 | 0.34 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1982 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 5U4S · 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 B4EFS5
- Elsewhere: RCSB PDB 5U4S · PDBe 5U4S · UniProt B4EFS5
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