MolNFT v1 · #163138 · protein
Piperideine-6-carboxylate dehydrogenase from streptomyces clavuligerus complexed with picolinic acid
6RTT · Semialdehyde dehydrogenase pcd: “Piperideine-6-carboxylate dehydrogenase from streptomyces clavuligerus complexed with picolinic acid”. X-ray diffraction, 2 ligands (6PC, SO4), 9 pockets (best druggability 0.85). MolNFT v1 #163138…
- PDB
- 6RTT
- 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
- 6PC, SO4
- Pockets
- 9 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Semialdehyde dehydrogenase pcd | protein | 508 | 43% helix, 20% strand | O85725 |
| B | Semialdehyde dehydrogenase pcd | protein | 499 | 43% helix, 22% strand | O85725 |
Ligands and binding sites
- 6PC · Pyridine-2-carboxylic acid · ligand · 5 copies · chains A, B
- SO4 · Sulfate ion · ion · 7 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1185 | 0.85 | 0.86 | 90 | 6PC, GOL |
| 2 | 542 | 0.73 | 0.81 | 50 | 6PC |
| 3 | 444 | 0.70 | 0.81 | 51 | 6PC |
| 4 | 411 | 0.63 | 0.77 | 48 | 6PC |
| 5 | 325 | 0.59 | 0.77 | 43 | empty |
Interfaces
1 interface between chains.
- A–B · 3304 Ų buried · 47 hydrogen bonds · protein-protein
Compared structures
- 6RTT · 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 6RTT · PDBe 6RTT · UniProt O85725
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