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Structure of pseudomonas nautica cytochrome C552, by mad method

Analyse Structure of pseudomonas nautica cytochrome C552, by mad method in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1CNO
Type: protein
Length: 689 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytochrome C552
UniProt: P82903
Ligands: HEC
Pockets: 4 · best druggability 0.84

Structure

x-ray diffraction · 2 distinct chains · 54% helix, 1% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, H	Cytochrome C552	protein	86	55% helix, 1% strand	P82903
G	Cytochrome C552	protein	87	54% helix, 1% strand	P82903

Ligands and binding sites

HEC · Heme C · ligand · 8 copies · chains A, B, E, C, D, H, F, G
GOL · Glycerol · additive · 3 copies · chains E, F, G

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

Pockets

4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	540	0.84	0.89	73	HEC
2	567	0.82	0.88	74	HEC
3	1127	0.82	0.83	116	HEC
4	599	0.82	0.87	78	HEC

Interfaces

15 interfaces between chains.

A–B · 927 Å² buried · 11 hydrogen bonds · protein-protein
C–D · 925 Å² buried · 14 hydrogen bonds · protein-protein
G–H · 919 Å² buried · 14 hydrogen bonds · protein-protein
E–F · 908 Å² buried · 13 hydrogen bonds · protein-protein
C–H · 430 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

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

Compared structures

1CNO · Structure of pseudomonas nautica cytochrome C552, by mad method · the same entry in another collection · chain H against H, TM-score 1.00
P82903 · AlphaFold monomer V2.0 prediction for cytochrome C-552 (P82903) · 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 P82903
Elsewhere: RCSB PDB 1CNO · PDBe 1CNO · UniProt P82903

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