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Lysine-ligated cytochrome C with F82H

Analyse Lysine-ligated cytochrome C with F82H in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4QAO
Type: protein
Length: 318 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytochrome C iso-1
UniProt: P00044
Ligands: HEM
Pockets: 5 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Cytochrome C iso-1	protein	106	39% helix, 9% strand	P00044

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 3 copies · chains A, B, C

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

Pockets

5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	756	0.81	0.84	83	HEM
2	252	0.75	0.88	37	HEM
3	286	0.73	0.86	40	HEM
4	251	0.54	0.76	27	empty
5	51	0.32	0.77	9	empty

Interfaces

3 interfaces between chains.

A–B · 296 Å² buried · 1 hydrogen bond · protein-protein
B–C · 216 Å² buried · 1 hydrogen bond · protein-protein
A–C · 197 Å² buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 cofactor (heme attachment).

Compared structures

4QAO · Lysine-ligated cytochrome c with F82H · the same entry in another collection · chain A against A, TM-score 1.00
P00044 · AlphaFold monomer V2.0 prediction for cytochrome C isoform 1 (P00044) · a predicted model of the same protein · chain A against A, TM-score 0.87

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 P00044
Elsewhere: RCSB PDB 4QAO · PDBe 4QAO · UniProt P00044

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