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Structure of recombinant human cytochrome C

Analyse Structure of recombinant human cytochrome C in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3ZCF
Type: protein
Length: 416 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytochrome C
UniProt: P99999
Ligands: HEC
Pockets: 5 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Cytochrome C	protein	104	41% helix, 2% strand	P99999

Ligands and binding sites

HEC · Heme C · ligand · 4 copies · chains A, B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	270	0.81	0.92	44	HEC
2	286	0.79	0.90	46	HEC
3	184	0.75	0.90	34	HEC
4	294	0.73	0.86	45	HEC
5	428	0.58	0.74	41	empty

Interfaces

4 interfaces between chains.

A–B · 429 Å² buried · 4 hydrogen bonds · protein-protein
C–D · 397 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 277 Å² buried · 0 hydrogen bonds · protein-protein
A–D · 56 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 5 cofactor (heme c attachment).

Compared structures

3ZCF · Structure of recombinant human cytochrome c · the same entry in another collection · chain D against D, TM-score 1.00
P99999 · AlphaFold monomer V2.0 prediction for cytochrome C (P99999) · a predicted model of the same protein · chain B against A, TM-score 1.00

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 P99999
Elsewhere: RCSB PDB 3ZCF · PDBe 3ZCF · UniProt P99999

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