Research workbench
PYRUVATE:FERREDOXIN oxidoreductase from moorella thermoacetica with lactyl-tpp bound
Analyse PYRUVATE:FERREDOXIN oxidoreductase from moorella thermoacetica with lactyl-tpp… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CIO
- Type
- protein
- Length
- 6,960 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate-ferredoxin oxidoreductase
- EC
- 1.2.7.-
- UniProt
- Q2RMD6
- Ligands
- SF4, TDL, TPP, MG, SO4
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 5 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pyruvate-ferredoxin oxidoreductase (EC 1.2.7.-) | protein | 1164 | 42% helix, 17% strand | Q2RMD6 |
| C | Pyruvate-ferredoxin oxidoreductase (EC 1.2.7.-) | protein | 1161 | 43% helix, 17% strand | Q2RMD6 |
| D | Pyruvate-ferredoxin oxidoreductase (EC 1.2.7.-) | protein | 1159 | 42% helix, 17% strand | Q2RMD6 |
| E | Pyruvate-ferredoxin oxidoreductase (EC 1.2.7.-) | protein | 1157 | 42% helix, 17% strand | Q2RMD6 |
| F | Pyruvate-ferredoxin oxidoreductase (EC 1.2.7.-) | protein | 1155 | 42% helix, 17% strand | Q2RMD6 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 18 copies · chains A, B, C, D, E, F
- TDL · 3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-2-(1-carboxy-1-hydroxyethyl)-5-(2-{[hydroxy(phosphonooxy) phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium · ligand · 4 copies · chains A, C, D, F
- TPP · Thiamine diphosphate · ligand · 2 copies · chains B, E
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, C, D, E, F
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 | 976 | 0.87 | 0.88 | 135 | SF4, TDL, MG |
| 2 | 901 | 0.86 | 0.88 | 127 | TPP, MG |
| 3 | 1005 | 0.86 | 0.87 | 140 | SF4, TDL, MG |
| 4 | 1196 | 0.85 | 0.86 | 142 | SF4, TPP, MG |
| 5 | 964 | 0.84 | 0.85 | 116 | SF4 |
Interfaces
6 interfaces between chains.
- E–F · 8503 Ų buried · 129 hydrogen bonds · protein-protein
- A–B · 8484 Ų buried · 127 hydrogen bonds · protein-protein
- C–D · 8432 Ų buried · 125 hydrogen bonds · protein-protein
- A–E · 1080 Ų buried · 12 hydrogen bonds · protein-protein
- C–F · 228 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6CIO · Pyruvate:ferredoxin oxidoreductase from Moorella thermoacetica with lactyl-TPP bound · the same entry in another collection · chain F against F, TM-score 1.00
- Q2RMD6 · AlphaFold monomer V2.0 prediction for PYRUVATE:FERREDOXIN oxidoreductase (Q2RMD6) · a predicted model of the same protein · chain C against A, TM-score 1.00
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 Q2RMD6
- Elsewhere: RCSB PDB 6CIO · PDBe 6CIO · UniProt Q2RMD6
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