MolNFT v1 · #127988 · protein
Crystal structure of cytochrome C in complex with P- METHYLPHOSPHONATOCALIX[4]ARENE
5NCV · Cytochrome C iso-1: “Crystal structure of cytochrome C in complex with P- METHYLPHOSPHONATOCALIX[4]ARENE”. X-ray diffraction, 3 ligands (8TE, HEC, CL), 3 pockets (best druggability 0.76). MolNFT v1 #127988 on GenesisL1: 3D…
- PDB
- 5NCV
- Type
- protein
- Length
- 208 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cytochrome C iso-1
- UniProt
- P00044
- Ligands
- 8TE, HEC, CL
- Pockets
- 3 · 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 | Cytochrome C iso-1 | protein | 104 | 42% helix, 2% strand | P00044 |
Ligands and binding sites
- 8TE · p-Methylphosphonatocalix[4]arene · ligand · 3 copies · chains A, B
- HEC · Heme C · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 197 | 0.76 | 0.90 | 34 | HEC |
| 2 | 203 | 0.76 | 0.90 | 36 | HEC |
| 3 | 54 | 0.32 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 520 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (heme c attachment).
Compared structures
- 5NCV · Crystal Structure of Cytochrome c in complex with p-Methylphosphonatocalix[4]arene · 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 5NCV · PDBe 5NCV · UniProt P00044
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