MolNFT v1 · #106063 · protein
K154 circular permutation of old yellow enzyme
4RNX · NADPH dehydrogenase 1: “K154 circular permutation of old yellow enzyme”. X-ray diffraction, 1 ligand (FMN), 7 pockets (best druggability 0.83). MolNFT v1 #106063 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4RNX
- Type
- protein
- Length
- 780 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
- 7 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | NADPH dehydrogenase 1 (EC 1.6.99.1) | protein | 390 | 35% helix, 14% strand | Q02899 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 249 | 0.83 | 0.95 | 33 | FMN |
| 2 | 239 | 0.82 | 0.94 | 33 | FMN |
| 3 | 108 | 0.35 | 0.73 | 26 | EDO |
| 4 | 52 | 0.33 | 0.78 | 16 | empty |
| 5 | 66 | 0.32 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 846 Ų buried · 13 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 4RNX · PDBe 4RNX · UniProt Q02899
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