MolNFT v1 · #84566 · protein

Structure of the Y46F mutant of human cytochrome C

3ZOO: “Structure of the Y46F mutant of human cytochrome C”. X-ray diffraction, 2 ligands (HEC, PO4), 5 pockets (best druggability 0.81). MolNFT v1 #84566 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3ZOO
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, PO4
Pockets: 5 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Cytochrome C	protein	104	42% helix, 2% strand	P99999

Ligands and binding sites

HEC · Heme C · ligand · 4 copies · chains A, B, C, D
PO4 · Phosphate ion · ion · 2 copies · chains A, D, B

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	293	0.81	0.92	46	HEC
2	295	0.78	0.90	49	HEC
3	194	0.75	0.90	35	HEC
4	263	0.73	0.87	45	HEC
5	587	0.64	0.75	57	empty

Interfaces

4 interfaces between chains.

C–D · 416 Å² buried · 2 hydrogen bonds · protein-protein
A–B · 414 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 276 Å² buried · 0 hydrogen bonds · protein-protein
A–D · 69 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 8 cofactor (heme c attachment).

Compared structures

3ZOO · Structure of the Y46F mutant of human cytochrome c · the same entry in another collection · chain B against B, TM-score 1.00
P99999 · AlphaFold monomer V2.0 prediction for cytochrome C (P99999) · a predicted model of the same protein · chain D 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 3ZOO · PDBe 3ZOO · UniProt P99999

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