MolNFT v1 · #163137 · protein
Piperideine-6-carboxylate dehydrogenase from streptomyces clavuligerus complexed with NAD+
6RTS · Semialdehyde dehydrogenase pcd: “Piperideine-6-carboxylate dehydrogenase from streptomyces clavuligerus complexed with NAD+”. X-ray diffraction, 2 ligands (NAD, SO4), 8 pockets (best druggability 0.86). MolNFT v1 #163137 on…
- PDB
- 6RTS
- Type
- protein
- Length
- 1,017 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Semialdehyde dehydrogenase pcd
- UniProt
- O85725
- Ligands
- NAD, SO4
- Pockets
- 8 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Semialdehyde dehydrogenase pcd | protein | 509 | 44% helix, 21% strand | O85725 |
| B | Semialdehyde dehydrogenase pcd | protein | 508 | 44% helix, 20% strand | O85725 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 8 copies · chains A, B
- GOL · Glycerol · additive · 5 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
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1138 | 0.86 | 0.87 | 86 | GOL |
| 2 | 942 | 0.78 | 0.80 | 95 | NAD, ACT |
| 3 | 989 | 0.77 | 0.79 | 98 | SO4, NAD, GOL, ACT |
| 4 | 183 | 0.44 | 0.74 | 23 | empty |
| 5 | 146 | 0.42 | 0.74 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 3638 Ų buried · 53 hydrogen bonds · protein-protein
Compared structures
- 6RTS · Piperideine-6-carboxylate dehydrogenase from Streptomyces clavuligerus complexed with NAD+ · 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 6RTS · PDBe 6RTS · UniProt O85725
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