Research workbench
G303 Circular Permutation of Old Yellow Enzyme with the Inhibitor p-Hydroxybenzaldehyde
Analyse G303 Circular Permutation of Old Yellow Enzyme with the Inhibitor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RNV
- Type
- protein
- Length
- 1,532 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.473
- Source
- Saccharomyces pastorianus
- Molecule
- NADPH dehydrogenase 1
- EC
- 1.6.99.1
- UniProt
- Q02899
- Ligands
- FMN, HBA
- Pockets
- 12 · best druggability 0.74
Structure
x-ray diffraction · resolution 2.473 · 1 distinct chain · 38% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | NADPH dehydrogenase 1 (EC 1.6.99.1) | protein | 383 | 38% helix, 14% strand | Q02899 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 4 copies · chains A, B, C, D
- HBA · P-hydroxybenzaldehyde · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 946 | 0.74 | 0.77 | 84 | FMN, HBA |
| 2 | 511 | 0.73 | 0.81 | 45 | FMN, HBA |
| 3 | 516 | 0.71 | 0.80 | 43 | FMN, HBA |
| 4 | 495 | 0.70 | 0.80 | 40 | FMN, HBA |
| 5 | 664 | 0.70 | 0.78 | 61 | empty |
Interfaces
5 interfaces between chains.
- A–B · 222 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 215 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 117 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 90 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 71 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4RNV · G303 circular permutation of old yellow enzyme with the inhibitor P- hydroxybenzaldehyde · the same entry in another collection · chain A against A, TM-score 1.00
- Q02899 · AlphaFold monomer V2.0 prediction for NADPH dehydrogenase 1 (Q02899) · a predicted model of the same protein · chain A against A, TM-score 0.76
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 Q02899
- Elsewhere: RCSB PDB 4RNV · PDBe 4RNV · UniProt Q02899
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