MolNFT v1 · #120711 · protein
Crystal structure of the complex between maize sulfite reductase and ferredoxin in the form-2 crystal
5H8Y · Sulfite reductase [ferredoxin], chloroplastic: “Crystal structure of the complex between maize sulfite reductase and ferredoxin in the form-2 crystal”. X-ray diffraction, 5 ligands (SF4, SRM, FES), 20 pockets (best druggability…
- PDB
- 5H8Y
- Type
- protein
- Length
- 2,418 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sulfite reductase [ferredoxin], chloroplastic; Ferredoxin-1, chloroplastic
- EC
- 1.8.7.1
- UniProt
- O23813, P27787
- Ligands
- SF4, SRM, FES, MG, CL
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 6 distinct chains · 37% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sulfite reductase [ferredoxin], chloroplastic (EC 1.8.7.1) | protein | 567 | 38% helix, 19% strand | O23813 |
| B | Sulfite reductase [ferredoxin], chloroplastic (EC 1.8.7.1) | protein | 565 | 38% helix, 19% strand | O23813 |
| C | Sulfite reductase [ferredoxin], chloroplastic (EC 1.8.7.1) | protein | 563 | 39% helix, 19% strand | O23813 |
| D | Sulfite reductase [ferredoxin], chloroplastic (EC 1.8.7.1) | protein | 554 | 39% helix, 19% strand | O23813 |
| E | Ferredoxin-1, chloroplastic | protein | 96 | 19% helix, 34% strand | P27787 |
| F | Ferredoxin-1, chloroplastic | protein | 73 | 14% helix, 19% strand | P27787 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 4 copies · chains A, B, C, D
- SRM · Siroheme · ligand · 4 copies · chains A, B, C, D
- FES · Fe2/s2 (inorganic) cluster · ligand · 2 copies · chains E, F
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1024 | 0.85 | 0.86 | 112 | SF4, SRM, CL |
| 2 | 1020 | 0.83 | 0.84 | 112 | SF4, SRM, CL |
| 3 | 833 | 0.79 | 0.82 | 97 | SF4, SRM, CL |
| 4 | 812 | 0.79 | 0.82 | 93 | SF4, SRM, CL |
| 5 | 527 | 0.66 | 0.77 | 40 | empty |
Interfaces
6 interfaces between chains.
- A–E · 572 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 531 Ų buried · 3 hydrogen bonds · protein-protein
- B–F · 450 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 320 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 309 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5H8Y · Crystal structure of the complex between maize sulfite reductase and ferredoxin in the… · the same entry in another collection · chain A against A, TM-score 1.00
- O23813 · AlphaFold monomer V2.0 prediction for sulfite reductase [ferredoxin], chloroplastic… · a predicted model of the same protein · chain D 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 E 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 O23813
- Every structure of UniProt P27787
- Elsewhere: RCSB PDB 5H8Y · PDBe 5H8Y · UniProt O23813 · UniProt P27787
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