Research workbench
P. stipitis OYE2.6-Y78W
Analyse P. stipitis OYE2.6-Y78W in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QAI
- Type
- protein
- Length
- 2,424 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADPH dehydrogenase
- UniProt
- A3LT82
- Ligands
- FMN
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | NADPH dehydrogenase | protein | 404 | 39% helix, 15% strand | A3LT82 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 242 | 0.80 | 0.92 | 36 | FMN |
| 2 | 1088 | 0.79 | 0.80 | 101 | FMN |
| 3 | 243 | 0.78 | 0.91 | 37 | FMN |
| 4 | 252 | 0.77 | 0.90 | 40 | FMN |
| 5 | 318 | 0.77 | 0.88 | 55 | FMN |
Interfaces
5 interfaces between chains.
- D–F · 866 Ų buried · 12 hydrogen bonds · protein-protein
- C–E · 823 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 417 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 308 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 226 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 cofactor (flavinylation).
Compared structures
- 4QAI · P. stipitis OYE2.6-Y78W · 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 A3LT82
- Elsewhere: RCSB PDB 4QAI · PDBe 4QAI · UniProt A3LT82
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