Research workbench

Tetrameric allochromatium vinosum cytochrome C'

Analyse Tetrameric allochromatium vinosum cytochrome C' in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5GYR
Type: protein
Length: 1,048 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytochrome C'
UniProt: P00154
Ligands: HEC
Pockets: 16 · best druggability 0.79

Structure

x-ray diffraction · 1 distinct chain · 71% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, E, F, I, J, M, N	Cytochrome C'	protein	131	71% helix, 5% strand	P00154

Ligands and binding sites

HEC · Heme C · ligand · 8 copies · chains A, N, B, E, J, F, I, M

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

Pockets

16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	700	0.79	0.83	94	empty
2	261	0.76	0.89	34	HEC
3	793	0.76	0.80	77	HEC
4	820	0.76	0.80	84	HEC
5	262	0.75	0.88	35	HEC

Interfaces

13 interfaces between chains.

E–J · 2686 Å² buried · 27 hydrogen bonds · protein-protein
A–N · 2683 Å² buried · 24 hydrogen bonds · protein-protein
I–J · 845 Å² buried · 7 hydrogen bonds · protein-protein
M–N · 833 Å² buried · 8 hydrogen bonds · protein-protein
E–F · 813 Å² buried · 5 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 cofactor (heme c attachment).

Compared structures

5GYR · Tetrameric Allochromatium vinosum cytochrome c' · the same entry in another collection · chain J against J, TM-score 1.00
P00154 · AlphaFold monomer V2.0 prediction for cytochrome C' (P00154) · a predicted model of the same protein · chain F 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 P00154
Elsewhere: RCSB PDB 5GYR · PDBe 5GYR · UniProt P00154

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