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Crystal structure of a cu-bound cytochrome CB562 variant in the presence of reductant

Analyse Crystal structure of a cu-bound cytochrome CB562 variant in the presence of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7TEP
Type: protein
Length: 424 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Soluble cytochrome B562
UniProt: P0ABE7
Ligands: HEC, CU
Pockets: 6 · best druggability 0.87

Structure

x-ray diffraction · 1 distinct chain · 76% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Soluble cytochrome B562	protein	106	76% helix, 0% strand	P0ABE7

Ligands and binding sites

HEC · Heme C · ligand · 4 copies · chains A, B, C, D
CU · Copper (II) ion · metal · 4 copies · chains A, B, C, D

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

Pockets

6 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	552	0.87	0.92	64	empty
2	152	0.65	0.86	22	HEC
3	227	0.63	0.82	28	HEC
4	191	0.62	0.82	37	HEC
5	158	0.57	0.82	30	HEC

Interfaces

6 interfaces between chains.

C–D · 871 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 807 Å² buried · 4 hydrogen bonds · protein-protein
A–D · 709 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 671 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 338 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 cofactor (heme c attachment).

Compared structures

7TEP · Crystal structure of a Cu-bound cytochrome cb562 variant in the presence of reductant · the same entry in another collection · chain D against D, TM-score 1.00
P0ABE7 · AlphaFold monomer V2.0 prediction for soluble cytochrome B562 (P0ABE7) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 P0ABE7
Elsewhere: RCSB PDB 7TEP · PDBe 7TEP · UniProt P0ABE7

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