MolNFT v1 · #82462 · protein

Crystal structure of cytochrome C552 from thermus thermophilus at pH 5.44

3VNW · Cytochrome C-552: “Crystal structure of cytochrome C552 from thermus thermophilus at pH 5.44”. X-ray diffraction, 1 ligand (HEM), 1 pocket (best druggability 0.75). MolNFT v1 #82462 on GenesisL1: 3D structure, binding sites and…

PDB: 3VNW
Type: protein
Length: 129 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytochrome C-552
UniProt: P04164
Ligands: HEM
Pockets: 1 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 47% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cytochrome C-552	protein	129	47% helix, 9% strand	P04164

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · 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	200	0.75	0.90	35	HEM

Modifications

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

Compared structures

3VNW · Crystal structure of cytochrome c552 from Thermus thermophilus at pH 5.44 · the same entry in another collection · chain A against A, TM-score 1.00
P04164 · AlphaFold monomer V2.0 prediction for cytochrome C-552 (P04164) · a predicted model of the same protein · chain A 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 P04164
Elsewhere: RCSB PDB 3VNW · PDBe 3VNW · UniProt P04164

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