MolNFT v1 · #91319 · protein
Structure of glycosylated glutaminyl cyclase from drosophila melanogaster
4F9U · CG32412: “Structure of glycosylated glutaminyl cyclase from drosophila melanogaster”. X-ray diffraction, 5 ligands (PBD, NAG, MAN), 4 pockets (best druggability 0.55). MolNFT v1 #91319 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4F9U
- Type
- protein
- Length
- 600 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CG32412
- EC
- 2.3.2.5, 3.4.-.-
- UniProt
- Q9VRQ9
- Ligands
- PBD, NAG, MAN, BMA, ZN
- Pockets
- 4 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CG32412 (EC 2.3.2.5, 3.4.-.-) | protein | 298 | 38% helix, 21% strand | Q9VRQ9 |
| B | CG32412 (EC 2.3.2.5, 3.4.-.-) | protein | 302 | 38% helix, 19% strand | Q9VRQ9 |
Ligands and binding sites
- PBD · 1-(3,4-dimethoxyphenyl)-3-[3-(1H-imidazol-1-yl)propyl]thiourea · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains B
- BMA · beta-D-mannopyranose · sugar
- ZN · Zinc ion · metal · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 145 | 0.55 | 0.81 | 19 | empty |
| 2 | 135 | 0.54 | 0.82 | 20 | empty |
| 3 | 327 | 0.51 | 0.73 | 42 | empty |
| 4 | 70 | 0.31 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 149 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 4F9U · Structure of glycosylated glutaminyl cyclase from Drosophila melanogaster · the same entry in another collection · 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 Q9VRQ9
- Elsewhere: RCSB PDB 4F9U · PDBe 4F9U · UniProt Q9VRQ9
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