Research workbench
Cross-linked complex between ferredoxin and ferredoxin-NADP+ reductase
Analyse Cross-linked complex between ferredoxin and ferredoxin-NADP+ reductase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3W5U
- Type
- protein
- Length
- 1,557 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ferredoxin; Ferredoxin-1, chloroplastic
- UniProt
- Q9SLP6, P27787
- Ligands
- FAD, FES
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 19% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Ferredoxin | protein | 296 | 25% helix, 31% strand | Q9SLP6 |
| B, H | Ferredoxin-1, chloroplastic | protein | 92 | 13% helix, 36% strand | P27787 |
| D | Ferredoxin-1, chloroplastic | protein | 95 | 13% helix, 35% strand | P27787 |
| F | Ferredoxin-1, chloroplastic | protein | 94 | 13% helix, 35% strand | P27787 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, D, B, C, E, H, F, G
- FES · Fe2/s2 (inorganic) cluster · ligand · 4 copies · chains B, D, F, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 624 | 0.78 | 0.84 | 95 | empty |
| 2 | 431 | 0.75 | 0.84 | 69 | empty |
| 3 | 342 | 0.71 | 0.84 | 54 | empty |
| 4 | 612 | 0.71 | 0.79 | 68 | FAD |
| 5 | 577 | 0.68 | 0.77 | 56 | FAD |
Interfaces
12 interfaces between chains.
- E–H · 825 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 819 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 804 Ų buried · 7 hydrogen bonds · protein-protein
- F–G · 804 Ų buried · 7 hydrogen bonds · protein-protein
- E–G · 448 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3W5U · Cross-linked complex between Ferredoxin and Ferredoxin-NADP+ reductase · the same entry in another collection · chain H against H, TM-score 1.00
- P27787 · AlphaFold monomer V2.0 prediction for ferredoxin-1, chloroplastic (P27787) · a predicted model of the same protein · chain H against A, TM-score 0.98
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 Q9SLP6
- Every structure of UniProt P27787
- Elsewhere: RCSB PDB 3W5U · PDBe 3W5U · UniProt Q9SLP6 · UniProt P27787
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