MolNFT v1 · #91320 · protein
Structure of C113A/C136A mutant variant of glycosylated glutaminyl cyclase from drosophila melanogaster
4F9V · CG32412: “Structure of C113A/C136A mutant variant of glycosylated glutaminyl cyclase from drosophila melanogaster”. X-ray diffraction, 5 ligands (PBD, NAG, MAN), 6 pockets (best druggability 0.74). MolNFT v1 #91320 on GenesisL1: 3D…
- PDB
- 4F9V
- Type
- protein
- Length
- 606 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
- 6 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | CG32412 (EC 2.3.2.5, 3.4.-.-) | protein | 307 | 39% helix, 20% strand | Q9VRQ9 |
| B | CG32412 (EC 2.3.2.5, 3.4.-.-) | protein | 299 | 38% helix, 20% 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
- BMA · beta-D-mannopyranose · sugar · 2 copies
- ZN · Zinc ion · metal · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 622 | 0.74 | 0.81 | 66 | PBD |
| 2 | 173 | 0.58 | 0.82 | 21 | empty |
| 3 | 161 | 0.53 | 0.80 | 19 | empty |
| 4 | 76 | 0.39 | 0.78 | 18 | empty |
| 5 | 86 | 0.33 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 423 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 glycan (N-glycosylation).
Compared structures
- 4F9V · Structure of C113A/C136A mutant variant of glycosylated glutaminyl cyclase from… · 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 4F9V · PDBe 4F9V · UniProt Q9VRQ9
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