MolNFT v1 · #72543 · protein

Crystal structure of dimeric cytochrome C from horse heart

3NBS: “Crystal structure of dimeric cytochrome C from horse heart”. X-ray diffraction, 2 ligands (HEC, PO4), 4 pockets (best druggability 0.82). MolNFT v1 #72543 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3NBS
Type: protein
Length: 416 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytochrome C
UniProt: P00004
Ligands: HEC, PO4
Pockets: 4 · best druggability 0.82

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Cytochrome C	protein	104	41% helix, 3% strand	P00004

Ligands and binding sites

HEC · Heme C · ligand · 4 copies · chains A, B, C, D
PO4 · Phosphate ion · ion · 2 copies · chains A, B, C, D
PG4 · Tetraethylene glycol · additive · 2 copies · chains A, C
PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B, C, 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, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	725	0.82	0.85	78	HEC, PEG
2	348	0.76	0.86	41	HEC
3	417	0.75	0.84	46	HEC, PEG
4	51	0.28	0.75	14	empty

Interfaces

6 interfaces between chains.

A–B · 2552 Å² buried · 21 hydrogen bonds · protein-protein
C–D · 2466 Å² buried · 25 hydrogen bonds · protein-protein
A–D · 466 Å² buried · 4 hydrogen bonds · protein-protein
B–C · 108 Å² buried · 6 hydrogen bonds · protein-protein
A–C · 79 Å² buried · 1 hydrogen bond · protein-protein

Modifications

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

Compared structures

3NBS · Crystal structure of dimeric cytochrome c from horse heart · the same entry in another collection · chain D against D, TM-score 1.00
P00004 · AlphaFold monomer V2.0 prediction for cytochrome C (P00004) · a predicted model of the same protein · chain C against A, TM-score 0.76

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 P00004
Elsewhere: RCSB PDB 3NBS · PDBe 3NBS · UniProt P00004

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