Research workbench
Cytochrome C in complex with sulfonato-CALIX[8]ARENE, P43212 form soaked with spermine
Analyse Cytochrome C in complex with sulfonato-CALIX[8]ARENE, P43212 form soaked with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GDA
- Type
- protein
- Length
- 108 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C iso-1
- UniProt
- P00044
- Ligands
- EVB, SPM, HEC, SO4
- Pockets
- 1 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cytochrome C iso-1 | protein | 108 | 41% helix, 4% strand | P00044 |
Ligands and binding sites
- EVB · sulfonato-calix[8]arene · ligand · 3 copies · chains A
- SPM · Spermine · ligand · 2 copies
- HEC · Heme C · ligand · chains A
- SO4 · Sulfate ion · ion · 9 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 180 | 0.77 | 0.92 | 30 | HEC |
Modifications
Observed in the structure: 2 cofactor (heme c attachment).
Compared structures
- 6GDA · Cytochrome c in complex with Sulfonato-calix[8]arene, P43212 form soaked with Spermine · the same entry in another collection · chain A against A, TM-score 1.00
- P00044 · AlphaFold monomer V2.0 prediction for cytochrome C isoform 1 (P00044) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P00044
- Elsewhere: RCSB PDB 6GDA · PDBe 6GDA · UniProt P00044
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