Research workbench
Crystal structure of NADP-dependent dehydrogenase from rhodobactersphaeroides in complex with NADP and sulfate
Analyse Crystal structure of NADP-dependent dehydrogenase from rhodobactersphaeroides… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZQB
- Type
- protein
- Length
- 629 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADP-dependent dehydrogenase
- EC
- 1.1.1.79, 1.1.1.81
- UniProt
- Q3IWN8
- Ligands
- NAP, SO4
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NADP-dependent dehydrogenase (EC 1.1.1.79, 1.1.1.81) | protein | 313 | 40% helix, 19% strand | Q3IWN8 |
| B | NADP-dependent dehydrogenase (EC 1.1.1.79, 1.1.1.81) | protein | 316 | 39% helix, 19% strand | Q3IWN8 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- PGE · Triethylene glycol · additive · chains A
- GOL · Glycerol · additive · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 712 | 0.76 | 0.81 | 78 | NAP, SO4, GOL |
| 2 | 569 | 0.74 | 0.82 | 61 | NAP, SO4 |
| 3 | 185 | 0.67 | 0.86 | 38 | empty |
| 4 | 327 | 0.63 | 0.79 | 33 | empty |
| 5 | 158 | 0.41 | 0.74 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 926 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 4ZQB · Crystal structure of NADP-dependent dehydrogenase from Rhodobactersphaeroides in complex… · 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 Q3IWN8
- Elsewhere: RCSB PDB 4ZQB · PDBe 4ZQB · UniProt Q3IWN8
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.