MolNFT v1 · #76820 · protein
Crystal structure of saccharomyces cerevisiae zeta-crystallin-like quinone oxidoreductase ZTA1 complexed with NADPH
3QWB · Probable quinone oxidoreductase: “Crystal structure of saccharomyces cerevisiae zeta-crystallin-like quinone oxidoreductase ZTA1 complexed with…”. X-ray diffraction, 1 ligand (NDP), 11 pockets (best druggability 0.80). MolNFT v1…
- PDB
- 3QWB
- Type
- protein
- Length
- 1,320 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable quinone oxidoreductase
- EC
- 1.6.5.5
- UniProt
- P38230
- Ligands
- NDP
- Pockets
- 11 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Probable quinone oxidoreductase (EC 1.6.5.5) | protein | 330 | 33% helix, 29% strand | P38230 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 548 | 0.80 | 0.86 | 59 | NDP, GOL |
| 2 | 576 | 0.80 | 0.86 | 57 | NDP, GOL |
| 3 | 602 | 0.80 | 0.85 | 61 | NDP, GOL |
| 4 | 591 | 0.79 | 0.85 | 61 | NDP, GOL |
| 5 | 585 | 0.65 | 0.76 | 52 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1266 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1262 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 510 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 36 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 13 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3QWB · Crystal structure of Saccharomyces cerevisiae Zeta-crystallin-like qui oxidoreductase… · the same entry in another collection · chain A against A, TM-score 1.00
- P38230 · AlphaFold monomer V2.0 prediction for probable quinone oxidoreductase (P38230) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P38230
- Elsewhere: RCSB PDB 3QWB · PDBe 3QWB · UniProt P38230
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