MolNFT v1 · #106062 · protein
Truncated version of the G303 circular permutation of old yellow enzyme
4RNW · NADPH dehydrogenase 1: “Truncated version of the G303 circular permutation of old yellow enzyme”. X-ray diffraction, 1 ligand (FMN), 2 pockets (best druggability 0.66). MolNFT v1 #106062 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4RNW
- Type
- protein
- Length
- 764 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NADPH dehydrogenase 1
- EC
- 1.6.99.1
- UniProt
- Q02899
- Ligands
- FMN
- Pockets
- 2 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NADPH dehydrogenase 1 (EC 1.6.99.1) | protein | 383 | 39% helix, 14% strand | Q02899 |
| B | NADPH dehydrogenase 1 (EC 1.6.99.1) | protein | 381 | 39% helix, 14% strand | Q02899 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 20 copies · chains A, B
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 426 | 0.66 | 0.79 | 46 | FMN, EPE, EDO |
| 2 | 441 | 0.66 | 0.78 | 52 | FMN, EPE, EDO |
Interfaces
1 interface between chains.
- A–B · 814 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4RNW · Truncated version of the G303 Circular Permutation of Old Yellow Enzyme · 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 B 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 4RNW · PDBe 4RNW · UniProt Q02899
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