Research workbench
Piperideine-6-carboxylate dehydrogenase from streptomyces clavuligerus
Analyse Piperideine-6-carboxylate dehydrogenase from streptomyces clavuligerus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RTR
- Type
- protein
- Length
- 1,001 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Semialdehyde dehydrogenase pcd
- UniProt
- O85725
- Ligands
- SO4
- Pockets
- 10 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Semialdehyde dehydrogenase pcd | protein | 505 | 42% helix, 21% strand | O85725 |
| B | Semialdehyde dehydrogenase pcd | protein | 496 | 43% helix, 22% strand | O85725 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
- ACT · Acetate ion · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1110 | 0.86 | 0.87 | 88 | GOL |
| 2 | 373 | 0.76 | 0.86 | 59 | empty |
| 3 | 509 | 0.73 | 0.82 | 49 | ACT |
| 4 | 355 | 0.56 | 0.75 | 35 | GOL |
| 5 | 332 | 0.55 | 0.75 | 41 | empty |
Interfaces
1 interface between chains.
- A–B · 3281 Ų buried · 46 hydrogen bonds · protein-protein
Compared structures
- 6RTR · Piperideine-6-carboxylate dehydrogenase from Streptomyces clavuligerus · 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 O85725
- Elsewhere: RCSB PDB 6RTR · PDBe 6RTR · UniProt O85725
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