Research workbench
Crystal structure of geranyltransferase from helicobacter pylori 26695
Analyse Crystal structure of geranyltransferase from helicobacter pylori 26695 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LLW
- Type
- protein
- Length
- 1,151 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Geranyltranstransferase (ispa)
- UniProt
- O25583
- Ligands
- SO4
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 74% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Geranyltranstransferase (ispa) | protein | 288 | 74% helix, 1% strand | O25583 |
| B | Geranyltranstransferase (ispa) | protein | 288 | 74% helix, 1% strand | O25583 |
| C | Geranyltranstransferase (ispa) | protein | 286 | 75% helix, 1% strand | O25583 |
| D | Geranyltranstransferase (ispa) | protein | 289 | 74% helix, 1% strand | O25583 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 9 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1163 | 0.76 | 0.79 | 105 | SO4 |
| 2 | 590 | 0.72 | 0.80 | 61 | SO4 |
| 3 | 599 | 0.70 | 0.79 | 60 | SO4 |
| 4 | 447 | 0.66 | 0.78 | 49 | SO4 |
| 5 | 121 | 0.44 | 0.77 | 23 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2383 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 2369 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 391 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 224 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 186 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3LLW · Crystal structure of geranyltransferase from helicobacter pylori 26695 · the same entry in another collection · chain C against C, 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 3LLW · PDBe 3LLW · UniProt O25583
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