MolNFT v1 · #157505 · protein

Oxidized rat cytochrome C mutant (S47E)

6N1O · Cytochrome C, somatic: “Oxidized rat cytochrome C mutant (S47E)”. X-ray diffraction, 2 ligands (HEC, FC6), 4 pockets (best druggability 0.83). MolNFT v1 #157505 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6N1O
Type: protein
Length: 416 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytochrome C, somatic
UniProt: P62898
Ligands: HEC, FC6
Pockets: 4 · best druggability 0.83

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, somatic	protein	104	42% helix, 2% strand	P62898

Ligands and binding sites

HEC · Heme C · ligand · 4 copies · chains A, D, B, C
FC6 · Hexacyanoferrate(3-) · ligand · 4 copies · chains A, B, C
EDO · 1,2-ethanediol · additive · 2 copies · chains A, D

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

Pockets

4 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	673	0.83	0.87	93	HEC, EDO
2	658	0.83	0.87	83	HEC, FC6
3	71	0.28	0.72	16	empty
4	56	0.25	0.72	19	empty

Interfaces

4 interfaces between chains.

A–D · 448 Å² buried · 3 hydrogen bonds · protein-protein
B–C · 398 Å² buried · 1 hydrogen bond · protein-protein
A–B · 279 Å² buried · 3 hydrogen bonds · protein-protein
C–D · 204 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

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

Compared structures

6N1O · Oxidized rat cytochrome c mutant (S47E) · the same entry in another collection · chain D against D, TM-score 1.00
P62898 · AlphaFold monomer V2.0 prediction for cytochrome C, somatic (P62898) · 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 P62898
Elsewhere: RCSB PDB 6N1O · PDBe 6N1O · UniProt P62898

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