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Crystal structure of trimeric cytochrome C from horse heart

Analyse Crystal structure of trimeric cytochrome C from horse heart in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3NBT
Type: protein
Length: 624 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytochrome C
UniProt: P00004
Ligands: HEC
Pockets: 8 · best druggability 0.89

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	Cytochrome C	protein	104	39% helix, 2% strand	P00004

Ligands and binding sites

HEC · Heme C · ligand · 6 copies · chains A, E, B, C, D, F
PG4 · Tetraethylene glycol · additive · 6 copies · chains A, C, B, E, D, F
PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains A, B, C, E
PGE · Triethylene glycol · additive · 2 copies · chains D, E, F

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

Pockets

8 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	1047	0.89	0.91	138	HEC, PEG, PGE
2	1175	0.88	0.89	135	HEC, PEG, PGE
3	141	0.55	0.81	25	empty
4	111	0.49	0.81	17	PG4
5	62	0.46	0.83	11	empty

Interfaces

10 interfaces between chains.

A–F · 1391 Å² buried · 10 hydrogen bonds · protein-protein
A–E · 1347 Å² buried · 7 hydrogen bonds · protein-protein
C–D · 1332 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 1326 Å² buried · 8 hydrogen bonds · protein-protein
E–F · 1310 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 cofactor (heme c attachment).

Compared structures

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

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