MolNFT v1 · #95825 · protein

X-ray structure of the cytochrome C-554 from chlorobaculum tepidum

4J20 · Cytochrome C-555: “X-ray structure of the cytochrome C-554 from chlorobaculum tepidum”. X-ray diffraction, 3 ligands (HEB, NA, SO4), 3 pockets (best druggability 0.71). MolNFT v1 #95825 on GenesisL1: 3D structure, binding sites and…

PDB: 4J20
Type: protein
Length: 176 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytochrome C-555
UniProt: Q8KG93
Ligands: HEB, NA, SO4
Pockets: 3 · best druggability 0.71

Structure

x-ray diffraction · 1 distinct chain · 60% helix, 5% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Cytochrome C-555	protein	88	60% helix, 5% strand	Q8KG93

Ligands and binding sites

HEB · Heme B/C · ligand · 2 copies · chains A, B
NA · Sodium ion · metal · chains A
SO4 · Sulfate ion · ion · chains A
IPA · Isopropyl alcohol · additive · 7 copies · chains A, B

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	153	0.71	0.90	35	HEB
2	160	0.68	0.87	34	HEB
3	117	0.42	0.76	25	IPA

Interfaces

1 interface between chains.

A–B · 225 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 4 covalent (covalent ligand).

Compared structures

4J20 · X-ray structure of the cytochrome c-554 from chlorobaculum tepidum · the same entry in another collection · chain B against B, TM-score 1.00
Q8KG93 · AlphaFold monomer V2.0 prediction for cytochrome C-555 (Q8KG93) · 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 Q8KG93
Elsewhere: RCSB PDB 4J20 · PDBe 4J20 · UniProt Q8KG93

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