MolNFT v1 · #111555 · protein
Crystal structure of double mutant Y115E Y117E human glutaminyl cyclase
4YU9 · Glutaminyl-peptide cyclotransferase: “Crystal structure of double mutant Y115E Y117E human glutaminyl cyclase”. X-ray diffraction, 2 ligands (ZN, SO4), 12 pockets (best druggability 0.72). MolNFT v1 #111555 on GenesisL1: 3D…
- PDB
- 4YU9
- Type
- protein
- Length
- 975 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
- ZN, SO4
- Pockets
- 12 · 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, 15% strand | Q16769 |
| B | Glutaminyl-peptide cyclotransferase (EC 2.3.2.5) | protein | 324 | 38% helix, 15% strand | Q16769 |
| C | Glutaminyl-peptide cyclotransferase (EC 2.3.2.5) | protein | 325 | 38% helix, 15% strand | Q16769 |
Ligands and binding sites
- 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 · 15 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 737 | 0.72 | 0.78 | 68 | SO4, EDO |
| 2 | 346 | 0.63 | 0.79 | 43 | EDO |
| 3 | 183 | 0.56 | 0.80 | 26 | EDO |
| 4 | 84 | 0.55 | 0.85 | 20 | empty |
| 5 | 93 | 0.53 | 0.84 | 19 | EDO |
Interfaces
2 interfaces between chains.
- A–B · 599 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 368 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4YU9 · Crystal Structure of double mutant Y115E Y117E human Glutaminyl Cyclase · 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 B 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 4YU9 · PDBe 4YU9 · UniProt Q16769
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