Research workbench

Yeast cytochrome C in complex with an octa-anionic CALIX[4]ARENE

Analyse Yeast cytochrome C in complex with an octa-anionic CALIX[4]ARENE in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6SUY
Type: protein
Length: 214 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytochrome C iso-1
UniProt: P00044
Ligands: HEC, LVT, NA, SO4
Pockets: 3 · 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	Cytochrome C iso-1	protein	107	41% helix, 2% strand	P00044

Ligands and binding sites

HEC · Heme C · ligand · 2 copies · chains A, B
LVT · octa-anionic calix[4]arene · ligand · 2 copies · chains A, B
NA · Sodium ion · metal · 2 copies
SO4 · Sulfate ion · ion · 5 copies · chains A, B

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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	188	0.78	0.92	32	HEC
2	191	0.76	0.91	35	HEC
3	52	0.24	0.72	9	empty

Interfaces

1 interface between chains.

A–B · 568 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 cofactor (heme c attachment).

Compared structures

6SUY · Yeast cytochrome c in complex with an octa-anionic calix[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 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 6SUY · PDBe 6SUY · UniProt P00044

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