MolNFT v2 · #225043 · protein
Crystal structure of human secretory glutaminyl cyclase in complex with (Z)-3-((1H-benzo[d]imidazol-5-yl)methylene)-4-hydroxyindolin-2-one
8XGT · Glutaminyl-peptide cyclotransferase: “Crystal structure of human secretory glutaminyl cyclase in complex with…”. X-ray diffraction at 2.813, 2 ligands (A1D48, ZN), 20 pockets (best druggability 0.85). MolNFT v2 #225043 on GenesisL1…
- PDB
- 8XGT
- Type
- protein
- Length
- 3,876 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.813
- Source
- Homo sapiens
- Molecule
- Glutaminyl-peptide cyclotransferase
- EC
- 2.3.2.5
- UniProt
- Q16769
- Ligands
- A1D48, ZN
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · resolution 2.813 · 1 distinct chain · 36% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A, C, D, E, F, G, H, I, J, K, L | Glutaminyl-peptide cyclotransferase (EC 2.3.2.5) | protein | 323 | 36% helix, 18% strand | Q16769 |
Ligands and binding sites
- A1D48 · (3~{Z})-3-(1~{H}-benzimidazol-5-ylmethylidene)-4-oxidanyl-1~{H}-indol-2-one · ligand · 12 copies · chains B, E, A, D, C, K, F, I, G, J, H, L
- ZN · Zinc ion · metal · 12 copies · chains B, A, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 984 | 0.85 | 0.86 | 103 | A1D48 |
| 2 | 1146 | 0.85 | 0.86 | 120 | A1D48 |
| 3 | 976 | 0.85 | 0.86 | 101 | A1D48 |
| 4 | 1038 | 0.85 | 0.85 | 105 | A1D48 |
| 5 | 793 | 0.85 | 0.87 | 96 | A1D48 |
Interfaces
29 interfaces between chains.
- G–J · 727 Ų buried · 5 hydrogen bonds · protein-protein
- A–K · 639 Ų buried · 10 hydrogen bonds · protein-protein
- F–H · 631 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 630 Ų buried · 11 hydrogen bonds · protein-protein
- D–E · 622 Ų buried · 10 hydrogen bonds · protein-protein
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 8XGT · PDBe 8XGT · UniProt Q16769
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