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Dimeric hydrogenobacter thermophilus cytochrome C552

Analyse Dimeric hydrogenobacter thermophilus cytochrome C552 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3VYM
Type: protein
Length: 80 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytochrome C-552
UniProt: P15452
Ligands: HEC
Pockets: 1 · best druggability 0.63

Structure

x-ray diffraction · 1 distinct chain · 50% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cytochrome C-552	protein	80	50% helix, 3% strand	P15452

Ligands and binding sites

HEC · Heme C · ligand · chains A

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	229	0.63	0.81	26	empty

Modifications

Observed in the structure: 2 cofactor (heme c attachment).

Compared structures

3VYM · Dimeric Hydrogenobacter thermophilus cytochrome c552 · the same entry in another collection · chain A against A, TM-score 1.00
P15452 · AlphaFold monomer V2.0 prediction for cytochrome C-552 (P15452) · a predicted model of the same protein · chain A against A, TM-score 0.73

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 P15452
Elsewhere: RCSB PDB 3VYM · PDBe 3VYM · UniProt P15452

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