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Structural and kinetic characterization of porphyromonas gingivalis glutaminyl cyclase
Analyse Structural and kinetic characterization of porphyromonas gingivalis glutaminyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CJG
- Type
- protein
- Length
- 565 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glutamine cyclotransferase-related protein
- UniProt
- Q7MT37
- Ligands
- DMD, MG, ZN, NO3
- Pockets
- 7 · best druggability 0.53
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glutamine cyclotransferase-related protein | protein | 289 | 38% helix, 20% strand | Q7MT37 |
| B | Glutamine cyclotransferase-related protein | protein | 276 | 39% helix, 20% strand | Q7MT37 |
Ligands and binding sites
- DMD · 5,6-dimethylbenzimidazole · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- NO3 · Nitrate ion · ion · 3 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 149 | 0.53 | 0.80 | 23 | DMD |
| 2 | 135 | 0.52 | 0.81 | 22 | DMD |
| 3 | 125 | 0.41 | 0.76 | 21 | NO3 |
| 4 | 90 | 0.40 | 0.78 | 18 | empty |
| 5 | 94 | 0.35 | 0.75 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 612 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7CJG · Structural and kinetic characterization of Porphyromonas gingivalis glutaminyl cyclase · 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 Q7MT37
- Elsewhere: RCSB PDB 7CJG · PDBe 7CJG · UniProt Q7MT37
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