Research workbench
Crystal structure of putative short-chain DEHYDROGENASE/REDUCTASE from burkholderia xenovorans LB400
Analyse Crystal structure of putative short-chain DEHYDROGENASE/REDUCTASE from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5K9Z
- Type
- protein
- Length
- 1,022 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative short-chain DEHYDROGENASE/REDUCTASE
- UniProt
- Q13HC1
- Pockets
- 13 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 50% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative short-chain DEHYDROGENASE/REDUCTASE | protein | 244 | 50% helix, 18% strand | Q13HC1 |
| B, C | Putative short-chain DEHYDROGENASE/REDUCTASE | protein | 266 | 51% helix, 17% strand | Q13HC1 |
| D | Putative short-chain DEHYDROGENASE/REDUCTASE | protein | 246 | 48% helix, 18% strand | Q13HC1 |
Ligands and binding sites
- GOL · Glycerol · additive · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 911 | 0.86 | 0.88 | 59 | empty |
| 2 | 754 | 0.75 | 0.80 | 91 | empty |
| 3 | 609 | 0.74 | 0.81 | 75 | empty |
| 4 | 95 | 0.47 | 0.81 | 20 | empty |
| 5 | 97 | 0.44 | 0.79 | 16 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1763 Ų buried · 21 hydrogen bonds · protein-protein
- A–D · 1717 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1598 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1597 Ų buried · 24 hydrogen bonds · protein-protein
- B–D · 1475 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 5K9Z · Crystal Structure of putative short-chain dehydrogenase/reductase from Burkholderia… · 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 Q13HC1
- Elsewhere: RCSB PDB 5K9Z · PDBe 5K9Z · UniProt Q13HC1
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