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Crystal structure of N64DEL mutant of nitrosomonas europaea cytochrome C552 (hexagonal space group)

Analyse Crystal structure of N64DEL mutant of nitrosomonas europaea cytochrome C552… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3ZOY
Type: protein
Length: 318 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cytochrome C-552
EC: 1.7.2.2
UniProt: P95339
Ligands: HEC
Pockets: 5 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 50% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Cytochrome C-552 (EC 1.7.2.2)	protein	80	50% helix, 3% strand	P95339
C, D	Cytochrome C-552 (EC 1.7.2.2)	protein	79	51% helix, 3% strand	P95339

Ligands and binding sites

HEC · Heme C · ligand · 4 copies · chains A, B, C, D

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

Pockets

5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	197	0.76	0.91	33	HEC
2	209	0.75	0.89	34	HEC
3	239	0.74	0.88	38	HEC
4	626	0.73	0.80	63	empty
5	257	0.73	0.86	41	HEC

Interfaces

5 interfaces between chains.

A–B · 530 Å² buried · 5 hydrogen bonds · protein-protein
C–D · 443 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 314 Å² buried · 2 hydrogen bonds · protein-protein
B–C · 228 Å² buried · 2 hydrogen bonds · protein-protein
A–D · 198 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

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

Compared structures

3ZOY · Crystal Structure of N64Del Mutant of Nitrosomonas europaea Cytochrome c552 (hexagonal… · the same entry in another collection · chain D against D, TM-score 1.00
P95339 · AlphaFold monomer V2.0 prediction for cytochrome C-552 (P95339) · a predicted model of the same protein · chain C against A, TM-score 0.98

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 P95339
Elsewhere: RCSB PDB 3ZOY · PDBe 3ZOY · UniProt P95339

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