MolNFT v1 · #32888 · protein
Crystal structure of the free radical intermediate of PYRUVATE:FERREDOXIN oxidoreductase from desulfovibrio africanus
2C3P · Pyruvate-ferredoxin oxidoreductase: “Crystal structure of the free radical intermediate of PYRUVATE:FERREDOXIN oxidoreductase from desulfovibrio…”. X-ray diffraction, 4 ligands (SF4, 1TP, MG), 20 pockets (best druggability 0.88).…
- PDB
- 2C3P
- Type
- protein
- Length
- 2,462 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, 1TP, MG, CA
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pyruvate-ferredoxin oxidoreductase (EC 1.2.7.1) | protein | 1231 | 41% helix, 16% strand | P94692 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 6 copies · chains A, B
- 1TP · 1-(2-{(2S,4R,5R)-3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-2-[(1S)-1-carboxy-1-hydroxyethyl]-4-methyl-1,3-thiazolidin-5-yl}ethoxy)-1, 1,3,3-tetrahydroxy-1lambda~5~-diphosphox-1-en-2-ium 3-oxide · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CA · Calcium ion · metal · 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, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1177 | 0.88 | 0.89 | 114 | empty |
| 2 | 1129 | 0.84 | 0.85 | 104 | empty |
| 3 | 182 | 0.82 | 0.97 | 36 | empty |
| 4 | 1100 | 0.82 | 0.83 | 105 | empty |
| 5 | 170 | 0.82 | 0.97 | 38 | 1TP, MG |
Interfaces
1 interface between chains.
- A–B · 13833 Ų buried · 204 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2C3P · CRYSTAL STRUCTURE OF THE FREE RADICAL INTERMEDIATE OF PYRUVATE:FERREDOXIN OXIDOREDUCTASE… · the same entry in another collection · chain B against B, TM-score 1.00
- P94692 · AlphaFold monomer V2.0 prediction for PYRUVATE:FERREDOXIN oxidoreductase (P94692) · a predicted model of the same protein · chain A 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 2C3P · PDBe 2C3P · UniProt P94692
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