Research workbench
Cytochrome C in complex with sulfonato-CALIX[8]ARENE, P31 form
Analyse Cytochrome C in complex with sulfonato-CALIX[8]ARENE, P31 form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GD8
- Type
- protein
- Length
- 432 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C iso-1
- UniProt
- P00044
- Ligands
- HEC, EVB
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Cytochrome C iso-1 | protein | 108 | 42% helix, 2% strand | P00044 |
Ligands and binding sites
- HEC · Heme C · ligand · 4 copies · chains A, B, C, D
- EVB · sulfonato-calix[8]arene · ligand · 4 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 199 | 0.78 | 0.92 | 33 | HEC |
| 2 | 200 | 0.77 | 0.92 | 35 | HEC |
| 3 | 195 | 0.77 | 0.91 | 33 | HEC |
| 4 | 193 | 0.76 | 0.91 | 33 | HEC |
| 5 | 68 | 0.29 | 0.73 | 13 | empty |
Interfaces
3 interfaces between chains.
- B–D · 58 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 31 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 14 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor (heme c attachment).
Compared structures
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 6GD8 · PDBe 6GD8 · UniProt P00044
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