Research workbench
Complex between ferredoxin and ferredoxin-NADP+ reductase from maize root
Analyse Complex between ferredoxin and ferredoxin-NADP+ reductase from maize root in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5H5J
- Type
- protein
- Length
- 715 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ferredoxin--NADP reductase; Ferredoxin-3, chloroplastic
- EC
- 1.18.1.2
- UniProt
- Q41736, P27788
- Ligands
- FAD, FES
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Ferredoxin--NADP reductase (EC 1.18.1.2) | protein | 309 | 27% helix, 28% strand | Q41736 |
| B | Ferredoxin-3, chloroplastic | protein | 97 | 19% helix, 32% strand | P27788 |
Ligands and binding sites
- FAD · Flavin-adenine dinucleotide · ligand · 2 copies · chains A, B, C
- FES · Fe2/s2 (inorganic) cluster · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 739 | 0.67 | 0.75 | 82 | FAD |
| 2 | 345 | 0.61 | 0.77 | 45 | FAD |
| 3 | 237 | 0.55 | 0.77 | 29 | empty |
| 4 | 117 | 0.36 | 0.73 | 24 | empty |
Interfaces
2 interfaces between chains.
- A–B · 649 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 178 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5H5J · Complex between ferredoxin and ferredoxin-NADP+ reductase from maize root · the same entry in another collection · chain A against A, TM-score 1.00
- P27788 · AlphaFold monomer V2.0 prediction for ferredoxin-3, chloroplastic (P27788) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q41736
- Every structure of UniProt P27788
- Elsewhere: RCSB PDB 5H5J · PDBe 5H5J · UniProt Q41736 · UniProt P27788
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