MolNFT v1 · #111645 · protein
Crystal structure of double mutant Y115E Y117E human glutaminyl cyclase in complex with inhibitor pbd-150
4YWY · Glutaminyl-peptide cyclotransferase: “Crystal structure of double mutant Y115E Y117E human glutaminyl cyclase in complex with inhibitor pbd-150”. X-ray diffraction, 4 ligands (PBD, ZN, SO4), 11 pockets (best druggability 0.72).…
- PDB
- 4YWY
- Type
- protein
- Length
- 978 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
- PBD, ZN, SO4, CL
- Pockets
- 11 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutaminyl-peptide cyclotransferase (EC 2.3.2.5) | protein | 326 | 37% helix, 16% strand | Q16769 |
| B | Glutaminyl-peptide cyclotransferase (EC 2.3.2.5) | protein | 326 | 38% helix, 15% strand | Q16769 |
| C | Glutaminyl-peptide cyclotransferase (EC 2.3.2.5) | protein | 326 | 40% helix, 15% strand | Q16769 |
Ligands and binding sites
- PBD · 1-(3,4-dimethoxyphenyl)-3-[3-(1H-imidazol-1-yl)propyl]thiourea · ligand · 3 copies · chains A, B, C
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C
- CL · Chloride ion · ion · chains A
- 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
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 793 | 0.72 | 0.78 | 77 | EDO, SO4 |
| 2 | 393 | 0.63 | 0.78 | 50 | EDO |
| 3 | 105 | 0.56 | 0.84 | 21 | EDO |
| 4 | 189 | 0.55 | 0.79 | 27 | empty |
| 5 | 123 | 0.53 | 0.82 | 21 | EDO |
Interfaces
2 interfaces between chains.
- A–B · 580 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 368 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4YWY · Crystal Structure of double mutant Y115E Y117E human Glutaminyl Cyclase in complex with… · 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 4YWY · PDBe 4YWY · UniProt Q16769
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.