MolNFT v1 · #104278 · protein

Lysine-ligated yeast iso-1 cytochrome C

4Q5P · Cytochrome C iso-1: “Lysine-ligated yeast iso-1 cytochrome C”. X-ray diffraction, 1 ligand (HEM), 5 pockets (best druggability 0.80). MolNFT v1 #104278 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4Q5P
Type: protein
Length: 314 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytochrome C iso-1
UniProt: P00044
Ligands: HEM
Pockets: 5 · best druggability 0.80

Structure

x-ray diffraction · 2 distinct chains · 39% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Cytochrome C iso-1	protein	106	38% helix, 9% strand	P00044
B, C	Cytochrome C iso-1	protein	104	39% helix, 8% strand	P00044

Ligands and binding sites

HEM · Protoporphyrin IX containing Fe · ligand · 3 copies · chains A, B, C

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

Pockets

5 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	687	0.80	0.84	70	HEM
2	241	0.75	0.89	38	HEM
3	350	0.74	0.85	43	HEM
4	98	0.40	0.77	16	empty
5	63	0.39	0.79	15	empty

Interfaces

3 interfaces between chains.

B–C · 358 Å² buried · 2 hydrogen bonds · protein-protein
A–C · 194 Å² buried · 4 hydrogen bonds · protein-protein
A–B · 148 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 1 cofactor (heme attachment).

Compared structures

4Q5P · Lysine-Ligated Yeast Iso-1 Cytochrome C · the same entry in another collection · chain A against A, TM-score 1.00
P00044 · AlphaFold monomer V2.0 prediction for cytochrome C isoform 1 (P00044) · a predicted model of the same protein · chain A against A, TM-score 0.87

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 P00044
Elsewhere: RCSB PDB 4Q5P · PDBe 4Q5P · UniProt P00044

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