MolNFT v1 · #185344 · protein
Cocrystal form I of a cytochrome C, sulfonato-THIACALIX[4]ARENE - zinc cluster
7PR3 · Cytochrome C iso-1: “Cocrystal form I of a cytochrome C, sulfonato-THIACALIX[4]ARENE - zinc cluster”. X-ray diffraction, 4 ligands (80M, HEC, ZN), 5 pockets (best druggability 0.78). MolNFT v1 #185344 on GenesisL1: 3D structure…
- PDB
- 7PR3
- 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
- 80M, HEC, ZN, PO4
- Pockets
- 5 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Cytochrome C iso-1 | protein | 107 | 41% helix, 2% strand | P00044 |
Ligands and binding sites
- 80M · sulfonato-thiacalix[4]arene · ligand · 6 copies · chains A, D, C, B
- HEC · Heme C · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 33 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 6 copies · chains C, D, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 194 | 0.78 | 0.92 | 33 | HEC |
| 2 | 212 | 0.77 | 0.91 | 34 | HEC |
| 3 | 189 | 0.76 | 0.91 | 32 | HEC |
| 4 | 392 | 0.72 | 0.83 | 52 | HEC |
| 5 | 91 | 0.31 | 0.73 | 18 | ZN, PO4 |
Interfaces
4 interfaces between chains.
- B–C · 54 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 30 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 23 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 19 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 cofactor (heme c attachment).
Compared structures
- 7PR3 · Cocrystal Form I of a cytochrome c, sulfonato-thiacalix[4]arene - zinc cluster · 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 B 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 7PR3 · PDBe 7PR3 · UniProt P00044
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