Research workbench
Crystal structure of the complex between pyruvate-ferredoxin oxidoreductase from desulfovibrio africanus and pyruvate.
Analyse Crystal structure of the complex between pyruvate-ferredoxin oxidoreductase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PDA
- Type
- protein
- Length
- 2,462 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (pyruvate-ferredoxin oxidoreductase)
- EC
- 1.2.7.1
- UniProt
- P94692
- Ligands
- SF4, TPP, PYR, MG, CA
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protein (pyruvate-ferredoxin oxidoreductase) (EC 1.2.7.1) | protein | 1231 | 40% helix, 16% strand | P94692 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 6 copies · chains A, B
- TPP · Thiamine diphosphate · ligand · 2 copies · chains A, B
- PYR · Pyruvic acid · 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 918 | 0.85 | 0.86 | 105 | empty |
| 2 | 1003 | 0.84 | 0.86 | 93 | empty |
| 3 | 344 | 0.84 | 0.94 | 31 | empty |
| 4 | 905 | 0.84 | 0.85 | 108 | empty |
| 5 | 235 | 0.84 | 0.96 | 36 | empty |
Interfaces
1 interface between chains.
- A–B · 13680 Ų buried · 235 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2PDA · Crystal structure of the complex between pyruvate-ferredoxin oxidoreductase from… · 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 0.96
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 2PDA · PDBe 2PDA · UniProt P94692
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