Research workbench
Crystal structure of ferredoxin NADP+ oxidoreductase from rhodopseudomonas palustris
Analyse Crystal structure of ferredoxin NADP+ oxidoreductase from rhodopseudomonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YGQ
- Type
- protein
- Length
- 681 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ferredoxin--NADP reductase
- EC
- 1.18.1.2
- UniProt
- Q6N2U4
- Ligands
- FAD
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 27% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ferredoxin--NADP reductase (EC 1.18.1.2) | protein | 341 | 27% helix, 29% strand | Q6N2U4 |
| B | Ferredoxin--NADP reductase (EC 1.18.1.2) | protein | 340 | 26% helix, 30% strand | Q6N2U4 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 223 | 0.78 | 0.91 | 44 | FAD |
| 2 | 203 | 0.76 | 0.91 | 45 | FAD |
| 3 | 124 | 0.64 | 0.87 | 22 | empty |
| 4 | 96 | 0.60 | 0.87 | 22 | empty |
| 5 | 256 | 0.54 | 0.76 | 38 | empty |
Interfaces
1 interface between chains.
- A–B · 1775 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 5YGQ · Crystal Structure of Ferredoxin NADP+ Oxidoreductase from Rhodopseudomonas palustris · the same entry in another collection · chain A against A, TM-score 1.00
- Q6N2U4 · AlphaFold monomer V2.0 prediction for ferredoxin--NADP reductase (Q6N2U4) · a predicted model of the same protein · chain A against A, TM-score 0.87
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 Q6N2U4
- Elsewhere: RCSB PDB 5YGQ · PDBe 5YGQ · UniProt Q6N2U4
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