Research workbench

Cu-bound structure of the engineered protein trimer, TRICYT3

Analyse Cu-bound structure of the engineered protein trimer, TRICYT3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6WZ3
Type: protein
Length: 318 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Soluble cytochrome B562
UniProt: P0ABE7
Ligands: HEC, CU, CL
Pockets: 7 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 79% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Soluble cytochrome B562	protein	106	79% helix, 0% strand	P0ABE7

Ligands and binding sites

HEC · Heme C · ligand · 3 copies · chains A, B, C
CU · Copper (II) ion · metal · chains A, B, C
CL · Chloride ion · ion · 7 copies · chains A, B, C
PEG · Di(hydroxyethyl)ether · additive · chains B

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

Pockets

7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	66	0.75	0.99	15	CL
2	328	0.63	0.79	50	HEC
3	168	0.59	0.82	24	HEC
4	148	0.56	0.81	21	HEC
5	201	0.52	0.77	35	CL

Interfaces

3 interfaces between chains.

A–C · 714 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 675 Å² buried · 11 hydrogen bonds · protein-protein
B–C · 654 Å² buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 cofactor (heme c attachment).

Compared structures

6WZ3 · Cu-bound structure of the engineered protein trimer, TriCyt3 · the same entry in another collection · chain A against A, TM-score 1.00
P0ABE7 · AlphaFold monomer V2.0 prediction for soluble cytochrome B562 (P0ABE7) · a predicted model of the same protein · chain B 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 6WZ3 · PDBe 6WZ3 · UniProt P0ABE7

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