Research workbench
Crystal structure of geranyltransferase from helicobacter pylori complexed with magnesium and isoprenyl diphosphate
Analyse Crystal structure of geranyltransferase from helicobacter pylori complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3Q1O
- Type
- protein
- Length
- 1,206 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Geranyltranstransferase (ispa)
- UniProt
- O25583
- Ligands
- DMA, MG, SO4
- Pockets
- 9 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 72% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Geranyltranstransferase (ispa) | protein | 303 | 72% helix, 1% strand | O25583 |
| C | Geranyltranstransferase (ispa) | protein | 301 | 73% helix, 1% strand | O25583 |
| D | Geranyltranstransferase (ispa) | protein | 299 | 71% helix, 1% strand | O25583 |
Ligands and binding sites
- DMA · Dimethylallyl diphosphate · ligand · 8 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 5 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 613 | 0.80 | 0.86 | 68 | MG, DMA |
| 2 | 498 | 0.79 | 0.86 | 48 | MG, DMA |
| 3 | 501 | 0.79 | 0.86 | 61 | MG, DMA |
| 4 | 555 | 0.77 | 0.84 | 72 | MG, DMA |
| 5 | 704 | 0.65 | 0.74 | 85 | empty |
Interfaces
4 interfaces between chains.
- C–D · 2405 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 484 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 302 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 264 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3Q1O · Crystal structure of geranyltransferase from helicobacter pylori complexed with magnesium… · 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 O25583
- Elsewhere: RCSB PDB 3Q1O · PDBe 3Q1O · UniProt O25583
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