MolNFT v1 · #163139 · protein
Piperideine-6-carboxylate dehydrogenase from streptomyces clavuligerus complexed with alpha-aminoadipic acid
6RTU · Semialdehyde dehydrogenase pcd: “Piperideine-6-carboxylate dehydrogenase from streptomyces clavuligerus complexed with alpha-aminoadipic acid”. X-ray diffraction, 2 ligands (UN1, SO4), 12 pockets (best druggability 0.86). MolNFT v1…
- PDB
- 6RTU
- Type
- protein
- Length
- 1,007 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Semialdehyde dehydrogenase pcd
- UniProt
- O85725
- Ligands
- UN1, SO4
- Pockets
- 12 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Semialdehyde dehydrogenase pcd | protein | 505 | 43% helix, 20% strand | O85725 |
| B | Semialdehyde dehydrogenase pcd | protein | 502 | 43% helix, 21% strand | O85725 |
Ligands and binding sites
- UN1 · 2-aminohexanedioic acid · ligand · chains A
- SO4 · Sulfate ion · ion · 10 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
- ACT · Acetate ion · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1078 | 0.86 | 0.87 | 85 | GOL, SO4 |
| 2 | 76 | 0.73 | 0.97 | 22 | UN1 |
| 3 | 526 | 0.73 | 0.81 | 49 | GOL |
| 4 | 270 | 0.55 | 0.77 | 32 | empty |
| 5 | 266 | 0.50 | 0.74 | 39 | empty |
Interfaces
1 interface between chains.
- A–B · 3633 Ų buried · 49 hydrogen bonds · protein-protein
Compared structures
- 6RTU · Piperideine-6-carboxylate dehydrogenase from Streptomyces clavuligerus complexed with… · 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 6RTU · PDBe 6RTU · UniProt O85725
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