MolNFT v1 · #32896 · protein
Crystal structure of the radical form of PYRUVATE:FERREDOXIN oxidoreductase from desulfovibrio africanus
2C3Y · Pyruvate-ferredoxin oxidoreductase: “Crystal structure of the radical form of PYRUVATE:FERREDOXIN oxidoreductase from desulfovibrio africanus”. X-ray diffraction, 5 ligands (SF4, HTL, MG), 20 pockets (best druggability 0.85). MolNFT…
- PDB
- 2C3Y
- Type
- protein
- Length
- 2,461 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate-ferredoxin oxidoreductase
- EC
- 1.2.7.1
- UniProt
- P94692
- Ligands
- SF4, HTL, MG, CA, CO2
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate-ferredoxin oxidoreductase (EC 1.2.7.1) | protein | 1231 | 41% helix, 16% strand | P94692 |
| B | Pyruvate-ferredoxin oxidoreductase (EC 1.2.7.1) | protein | 1230 | 40% helix, 16% strand | P94692 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 6 copies · chains A, B
- HTL · 2-acetyl-thiamine diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
- CO2 · Carbon dioxide · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 959 | 0.85 | 0.87 | 86 | empty |
| 2 | 318 | 0.85 | 0.95 | 29 | empty |
| 3 | 1166 | 0.84 | 0.85 | 98 | empty |
| 4 | 193 | 0.83 | 0.97 | 37 | empty |
| 5 | 1173 | 0.82 | 0.83 | 116 | empty |
Interfaces
1 interface between chains.
- A–B · 13672 Ų buried · 196 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2C3Y · CRYSTAL STRUCTURE OF THE RADICAL FORM OF PYRUVATE:FERREDOXIN OXIDOREDUCTASE FROM… · the same entry in another collection · chain A against A, TM-score 1.00
- P94692 · AlphaFold monomer V2.0 prediction for PYRUVATE:FERREDOXIN oxidoreductase (P94692) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P94692
- Elsewhere: RCSB PDB 2C3Y · PDBe 2C3Y · UniProt P94692
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