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
- 3W5V
- Type
- protein
- Length
- 786 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ferredoxin; Ferredoxin-1, chloroplastic
- UniProt
- Q9SLP6, P27787
- Ligands
- FAD, FES
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Ferredoxin | protein | 297 | 22% helix, 29% strand | Q9SLP6 |
| B, D | Ferredoxin-1, chloroplastic | protein | 96 | 19% helix, 34% strand | P27787 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, C
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 776 | 0.65 | 0.74 | 67 | empty |
| 2 | 394 | 0.60 | 0.76 | 28 | empty |
| 3 | 213 | 0.53 | 0.77 | 37 | empty |
| 4 | 234 | 0.52 | 0.76 | 39 | FAD |
| 5 | 92 | 0.32 | 0.73 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–C · 386 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 239 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 65 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3W5V · Cross-linked complex between Ferredoxin and Ferredoxin-NADP+ reductase · the same entry in another collection · chain A against A, TM-score 1.00
- P27787 · AlphaFold monomer V2.0 prediction for ferredoxin-1, chloroplastic (P27787) · a predicted model of the same protein · chain B 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 3W5V · PDBe 3W5V · UniProt Q9SLP6 · UniProt P27787
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