Research workbench
Crystal structure of human secretory glutaminyl cyclase in complex with PBD150
Analyse Crystal structure of human secretory glutaminyl cyclase in complex with PBD150 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PBB
- Type
- protein
- Length
- 646 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutaminyl-peptide cyclotransferase
- EC
- 2.3.2.5
- UniProt
- Q16769
- Ligands
- PBD, ZN
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Glutaminyl-peptide cyclotransferase (EC 2.3.2.5) | protein | 323 | 39% helix, 18% strand | Q16769 |
Ligands and binding sites
- PBD · 1-(3,4-dimethoxyphenyl)-3-[3-(1H-imidazol-1-yl)propyl]thiourea · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 467 | 0.73 | 0.82 | 65 | empty |
| 2 | 95 | 0.52 | 0.83 | 20 | empty |
| 3 | 71 | 0.43 | 0.81 | 17 | PBD |
| 4 | 57 | 0.40 | 0.81 | 17 | PBD |
| 5 | 106 | 0.35 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 450 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3PBB · Crystal structure of human secretory glutaminyl cyclase in complex with PBD150 · 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 3PBB · PDBe 3PBB · UniProt Q16769
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