Research workbench

Crystal structure of human glutaminyl cyclase variant Y115E-Y117E in complex with SEN177

Analyse Crystal structure of human glutaminyl cyclase variant Y115E-Y117E in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6GBX
Type: protein
Length: 984 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glutaminyl-peptide cyclotransferase
EC: 2.3.2.5
UniProt: Q16769
Ligands: S77, ZN, SO4
Pockets: 13 · best druggability 0.68

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Glutaminyl-peptide cyclotransferase (EC 2.3.2.5)	protein	328	38% helix, 16% strand	Q16769

Ligands and binding sites

S77 · 2-fluoranyl-5-[2-[4-(4-methyl-1,2,4-triazol-3-yl) piperidin-1-yl]pyridin-3-yl]pyridine · ligand · 3 copies · chains A, B, C
ZN · Zinc ion · metal · 3 copies · chains A, B, C
SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
EDO · 1,2-ethanediol · additive · 20 copies · chains A, B, C

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

Pockets

13 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	563	0.68	0.78	59	SO4, EDO
2	389	0.64	0.78	57	empty
3	96	0.56	0.85	23	EDO
4	184	0.54	0.79	27	EDO
5	88	0.53	0.84	20	EDO

Interfaces

2 interfaces between chains.

B–C · 699 Å² buried · 12 hydrogen bonds · protein-protein
A–C · 409 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

6GBX · Crystal structure of human glutaminyl cyclase variant Y115E-Y117E in complex with SEN177 · the same entry in another collection · chain A against A, TM-score 1.00
Q16769 · AlphaFold monomer V2.0 prediction for glutaminyl-peptide cyclotransferase (Q16769) · a predicted model of the same protein · chain A against A, TM-score 1.00

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 Q16769
Elsewhere: RCSB PDB 6GBX · PDBe 6GBX · UniProt Q16769

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.