Research workbench
Pseudopaline dehydrogenase with (S)-pseudopaline soaked 1 hour
Analyse Pseudopaline dehydrogenase with (S)-pseudopaline soaked 1 hour in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PBP
- Type
- protein
- Length
- 850 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pseudopaline dehydrogenase
- EC
- 1.5.1.-
- UniProt
- Q9HUX5
- Ligands
- NAP, O7J
- Pockets
- 8 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pseudopaline dehydrogenase (EC 1.5.1.-) | protein | 425 | 46% helix, 15% strand | Q9HUX5 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- O7J · N-[(1S)-1-carboxy-3-{[(1S)-1-carboxy-2-(1H-imidazol-5-yl)ethyl]amino}propyl]-L-glutamic acid · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 8 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 | 1104 | 0.79 | 0.81 | 94 | NAP, O7J, EDO |
| 2 | 994 | 0.78 | 0.80 | 80 | NAP, O7J, EDO |
| 3 | 184 | 0.66 | 0.85 | 27 | empty |
| 4 | 133 | 0.46 | 0.77 | 18 | empty |
| 5 | 74 | 0.34 | 0.76 | 20 | EDO |
Interfaces
1 interface between chains.
- A–B · 1470 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
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 Q9HUX5
- Elsewhere: RCSB PDB 6PBP · PDBe 6PBP · UniProt Q9HUX5
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