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Crystal structure of dimeric yeast iso-1-cytochrome C with CYMAL6

Analyse Crystal structure of dimeric yeast iso-1-cytochrome C with CYMAL6 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5T7H
Type: protein
Length: 424 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytochrome C iso-1
UniProt: P00044
Ligands: ZE7, HEC, SO4
Pockets: 6 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Cytochrome C iso-1	protein	106	42% helix, 4% strand	P00044

Ligands and binding sites

ZE7 · 6-cyclohexylhexan-1-ol · ligand · 4 copies · chains A, B, C, D
HEC · Heme C · ligand · 4 copies · chains A, D, B, C
SO4 · Sulfate ion · ion · 9 copies · chains A, B, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	469	0.79	0.87	50	ZE7, HEC
2	404	0.78	0.87	38	ZE7, HEC
3	461	0.78	0.85	46	ZE7, HEC
4	439	0.77	0.85	44	ZE7, HEC
5	62	0.32	0.76	18	SO4

Interfaces

4 interfaces between chains.

A–D · 2547 Å² buried · 23 hydrogen bonds · protein-protein
B–C · 2531 Å² buried · 28 hydrogen bonds · protein-protein
C–D · 370 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 367 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 cofactor (heme c attachment).

Compared structures

5T7H · Crystal structure of dimeric yeast iso-1-cytochrome C with CYMAL6 · 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 0.70

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 5T7H · PDBe 5T7H · UniProt P00044

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