MolNFT v1 · #147421 · protein

Human cytochrome C G41T

6ECJ: “Human cytochrome C G41T”. X-ray diffraction, 1 ligand (HEC), 12 pockets (best druggability 0.78). MolNFT v1 #147421 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6ECJ
Type: protein
Length: 832 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytochrome C
UniProt: P99999
Ligands: HEC
Pockets: 12 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G, H	Cytochrome C	protein	104	40% helix, 2% strand	P99999

Ligands and binding sites

HEC · Heme C · ligand · 8 copies · chains A, B, C, D, E, F, G, H

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

Pockets

12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	239	0.78	0.91	39	HEC
2	544	0.77	0.84	64	HEC
3	206	0.77	0.91	32	HEC
4	195	0.76	0.91	32	HEC
5	195	0.75	0.90	30	HEC

Interfaces

8 interfaces between chains.

A–B · 433 Å² buried · 13 hydrogen bonds · protein-protein
B–G · 389 Å² buried · 6 hydrogen bonds · protein-protein
B–C · 372 Å² buried · 7 hydrogen bonds · protein-protein
E–G · 359 Å² buried · 5 hydrogen bonds · protein-protein
B–D · 168 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 cofactor (heme c attachment).

Compared structures

6ECJ · Human cytochrome c G41T · the same entry in another collection · chain H against H, TM-score 1.00
P99999 · AlphaFold monomer V2.0 prediction for cytochrome C (P99999) · 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 P99999
Elsewhere: RCSB PDB 6ECJ · PDBe 6ECJ · UniProt P99999

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