Research workbench
Structure determination of the ferricytochrome C2 from rhodopseudomonas palustris
Analyse Structure determination of the ferricytochrome C2 from rhodopseudomonas… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1FJ0
- Type
- protein
- Length
- 456 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C2
- UniProt
- P00091
- Ligands
- HEC, SO4
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Cytochrome C2 | protein | 114 | 46% helix, 2% strand | P00091 |
Ligands and binding sites
- HEC · Heme C · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 2 copies · chains A, C
- GOL · Glycerol · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 222 | 0.79 | 0.92 | 37 | HEC |
| 2 | 237 | 0.78 | 0.91 | 42 | HEC |
| 3 | 184 | 0.76 | 0.92 | 33 | HEC |
| 4 | 186 | 0.72 | 0.88 | 34 | HEC |
| 5 | 125 | 0.38 | 0.74 | 25 | empty |
Interfaces
4 interfaces between chains.
- C–D · 395 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 394 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 140 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 131 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor, 4 modified (heme c attachment, cyclization).
Compared structures
- 1FJ0 · Structure determination of the ferricytochrome C2 from rhodopseudomonas palustris · the same entry in another collection · chain D against D, TM-score 1.00
- P00091 · AlphaFold monomer V2.0 prediction for cytochrome C2 (P00091) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P00091
- Elsewhere: RCSB PDB 1FJ0 · PDBe 1FJ0 · UniProt P00091
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