MolNFT v1 · #88755 · protein

Nitrosyl complex of the D121A variant of cytochrome C prime from alcaligenes xylosoxidans

4D4N · Cytochrome C': “Nitrosyl complex of the D121A variant of cytochrome C prime from alcaligenes xylosoxidans”. X-ray diffraction, 2 ligands (HEC, NO), 1 pocket (best druggability 0.67). MolNFT v1 #88755 on GenesisL1: 3D structure…

PDB: 4D4N
Type: protein
Length: 125 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytochrome C'
UniProt: P00138
Ligands: HEC, NO
Pockets: 1 · best druggability 0.67

Structure

x-ray diffraction · 1 distinct chain · 74% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cytochrome C'	protein	125	74% helix, 2% strand	P00138

Ligands and binding sites

HEC · Heme C · ligand · chains A
NO · Nitric oxide · ion · 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	238	0.67	0.84	30	HEC, NO

Modifications

Observed in the structure: 2 cofactor, 1 modified (heme c attachment, cyclization).

Compared structures

4D4N · Nitrosyl complex of the D121A variant of cytochrome c prime from Alcaligenes xylosoxidans · the same entry in another collection · chain A against A, TM-score 1.00
P00138 · AlphaFold monomer V2.0 prediction for cytochrome C' (P00138) · 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 P00138
Elsewhere: RCSB PDB 4D4N · PDBe 4D4N · UniProt P00138

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