Research workbench

Crystal structure of N63T yeast iso-1-cytochrome c

Analyse Crystal structure of N63T yeast iso-1-cytochrome c in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7MRI
Type: protein
Length: 321 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.46
Source: Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Molecule: Cytochrome c isoform 1
UniProt: P00044
Ligands: HEC
Pockets: 4 · best druggability 0.77

Structure

x-ray diffraction · resolution 2.46 · 1 distinct chain · 41% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E	Cytochrome c isoform 1	protein	107	41% helix, 2% strand	P00044

Ligands and binding sites

HEC · Heme C · ligand · 3 copies · chains A, C, E

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

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	198	0.77	0.91	31	HEC
2	176	0.74	0.91	31	HEC
3	636	0.74	0.80	75	HEC
4	85	0.34	0.75	19	empty

Interfaces

3 interfaces between chains.

C–E · 347 Å² buried · 4 hydrogen bonds · protein-protein
A–C · 217 Å² buried · 1 hydrogen bond · protein-protein
A–E · 76 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 6 cofactor (heme c attachment).

Compared structures

7MRI · Crystal structure of N63T yeast iso-1-cytochrome C · 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 C 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 7MRI · PDBe 7MRI · UniProt P00044

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.