MolNFT v1 · #106060 · protein
G303 circular permutation of old yellow enzyme
4RNU · NADPH dehydrogenase 1: “G303 circular permutation of old yellow enzyme”. X-ray diffraction, 2 ligands (FMN, PO4), 9 pockets (best druggability 0.73). MolNFT v1 #106060 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4RNU
- Type
- protein
- Length
- 1,527 residues
- Chains
- 4
- 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, PO4
- Pockets
- 9 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 35% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NADPH dehydrogenase 1 (EC 1.6.99.1) | protein | 383 | 37% helix, 15% strand | Q02899 |
| B | NADPH dehydrogenase 1 (EC 1.6.99.1) | protein | 380 | 36% helix, 14% strand | Q02899 |
| C | NADPH dehydrogenase 1 (EC 1.6.99.1) | protein | 385 | 35% helix, 15% strand | Q02899 |
| D | NADPH dehydrogenase 1 (EC 1.6.99.1) | protein | 379 | 32% helix, 13% strand | Q02899 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 4 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 544 | 0.73 | 0.81 | 44 | FMN, PO4 |
| 2 | 829 | 0.72 | 0.77 | 85 | empty |
| 3 | 437 | 0.68 | 0.80 | 44 | FMN, PO4 |
| 4 | 547 | 0.68 | 0.78 | 48 | FMN, PO4 |
| 5 | 666 | 0.67 | 0.76 | 56 | empty |
Interfaces
5 interfaces between chains.
- B–D · 246 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 157 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 80 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 76 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 74 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
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 4RNU · PDBe 4RNU · UniProt Q02899
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