MolNFT v1 · #124784 · protein
Crystal structure of cytochrome C - phenyl-TRISULFONATOCALIX[4]ARENE complex
5KPF · Cytochrome C iso-1: “Crystal structure of cytochrome C - phenyl-TRISULFONATOCALIX[4]ARENE complex”. X-ray diffraction, 3 ligands (HEC, 6VJ, NO3), 4 pockets (best druggability 0.77). MolNFT v1 #124784 on GenesisL1: 3D structure…
- PDB
- 5KPF
- Type
- protein
- Length
- 216 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C iso-1
- UniProt
- P00044
- Ligands
- HEC, 6VJ, NO3
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cytochrome C iso-1 | protein | 108 | 44% helix, 2% strand | P00044 |
Ligands and binding sites
- HEC · Heme C · ligand · 2 copies · chains A, B
- 6VJ · Phenyl-trisulfonatocalix[4]arene · ligand · chains B
- NO3 · Nitrate ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 191 | 0.77 | 0.91 | 30 | HEC |
| 2 | 217 | 0.76 | 0.90 | 39 | HEC |
| 3 | 123 | 0.47 | 0.79 | 23 | empty |
| 4 | 113 | 0.45 | 0.79 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 556 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (heme c attachment).
Compared structures
- 5KPF · Crystal structure of cytochrome c - Phenyl-trisulfonatocalix[4]arene complex · 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 5KPF · PDBe 5KPF · UniProt P00044
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