MolNFT v1 · #173814 · protein
Structure of cytochrome C in complex with a P-benzyl-sulfonato- CALIX[8]ARENE-peg pseudorotaxane
7BBT · Cytochrome C iso-1: “Structure of cytochrome C in complex with a P-benzyl-sulfonato- CALIX[8]ARENE-peg pseudorotaxane”. X-ray diffraction, 2 ligands (HEC, T8W), 7 pockets (best druggability 0.76). MolNFT v1 #173814 on GenesisL1: 3D…
- PDB
- 7BBT
- Type
- protein
- Length
- 428 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C iso-1
- UniProt
- P00044
- Ligands
- HEC, T8W
- Pockets
- 7 · best druggability 0.76
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 | 107 | 42% helix, 2% strand | P00044 |
Ligands and binding sites
- HEC · Heme C · ligand · 4 copies · chains A, B, C, D
- T8W · 4-[[49,50,51,52,53,54,55,56-octahydroxy-11,17,23,29,35, 41,47-heptakis[(4-sulfonatophenyl)methyl]-5-nonacyclo[43.3.1.13,7.19,13.115,19.121,25.127,31.133, 37.139,43]hexapentaconta-1(49),3,5,7(56),9,11,13(55), 15,17,19(54),21,23,25(53),27,29,31(52),33,35,37(51), 39,41,43(50),45,47-tetracosaenyl]methyl]benzenesulfonate · ligand · 3 copies · chains C, D
- 15P · Polyethylene glycol (N=34) · additive · chains 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 182 | 0.76 | 0.92 | 29 | HEC |
| 2 | 191 | 0.76 | 0.91 | 31 | HEC |
| 3 | 276 | 0.72 | 0.86 | 45 | HEC |
| 4 | 299 | 0.72 | 0.85 | 48 | HEC |
| 5 | 147 | 0.51 | 0.80 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–C · 484 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 260 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 193 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor (heme c attachment).
Compared structures
- 7BBT · Structure of cytochrome c in complex with a p-benzyl-sulfonato-calix[8]arene-PEG… · the same entry in another collection · chain D against D, 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 7BBT · PDBe 7BBT · UniProt P00044
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