Research workbench
Pseudopaline dehydrogenase with NADP+ bound
Analyse Pseudopaline dehydrogenase with NADP+ bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PBM
- Type
- protein
- Length
- 851 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
- Pockets
- 7 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pseudopaline dehydrogenase (EC 1.5.1.-) | protein | 426 | 46% helix, 15% strand | Q9HUX5 |
| 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
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1182 | 0.80 | 0.81 | 94 | NAP, EDO |
| 2 | 1156 | 0.75 | 0.77 | 98 | NAP, EDO |
| 3 | 153 | 0.65 | 0.87 | 29 | EDO |
| 4 | 142 | 0.51 | 0.79 | 20 | empty |
| 5 | 88 | 0.36 | 0.75 | 21 | EDO |
Interfaces
1 interface between chains.
- A–B · 1519 Ų buried · 10 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 6PBM · PDBe 6PBM · UniProt Q9HUX5
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