Research workbench
Crystal structure of PYRUVATE:FERREDOXIN oxidoreductase from moorella thermoacetica
Analyse Crystal structure of PYRUVATE:FERREDOXIN oxidoreductase from moorella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CIN
- Type
- protein
- Length
- 6,975 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, TPP, MG, SO4
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 6 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate-ferredoxin oxidoreductase (EC 1.2.7.-) | protein | 1163 | 42% helix, 17% strand | Q2RMD6 |
| B | Pyruvate-ferredoxin oxidoreductase (EC 1.2.7.-) | protein | 1169 | 43% helix, 16% strand | Q2RMD6 |
| C | Pyruvate-ferredoxin oxidoreductase (EC 1.2.7.-) | protein | 1163 | 42% helix, 17% strand | Q2RMD6 |
| D | Pyruvate-ferredoxin oxidoreductase (EC 1.2.7.-) | protein | 1157 | 42% helix, 17% strand | Q2RMD6 |
| E | Pyruvate-ferredoxin oxidoreductase (EC 1.2.7.-) | protein | 1165 | 43% helix, 17% strand | Q2RMD6 |
| F | Pyruvate-ferredoxin oxidoreductase (EC 1.2.7.-) | protein | 1158 | 42% helix, 17% strand | Q2RMD6 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 18 copies · chains A, B, C, D, E, F
- TPP · Thiamine diphosphate · ligand · 6 copies · chains A, B, C, D, E, F
- 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 | 969 | 0.87 | 0.88 | 132 | SF4, TPP, MG |
| 2 | 1031 | 0.87 | 0.88 | 139 | SF4, TPP, MG |
| 3 | 713 | 0.85 | 0.89 | 95 | empty |
| 4 | 1155 | 0.85 | 0.86 | 151 | SF4, TPP, MG |
| 5 | 1149 | 0.85 | 0.86 | 144 | SF4, TPP, MG, SO4 |
Interfaces
6 interfaces between chains.
- A–B · 8547 Ų buried · 133 hydrogen bonds · protein-protein
- C–D · 8513 Ų buried · 134 hydrogen bonds · protein-protein
- E–F · 8504 Ų buried · 119 hydrogen bonds · protein-protein
- A–C · 1024 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 174 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6CIN · Crystal structure of pyruvate:ferredoxin oxidoreductase from Moorella thermoacetica · 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 6CIN · PDBe 6CIN · UniProt Q2RMD6
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