Research workbench
Crystal structure of helicobacter pylori undecaprenyl pyrophosphate synthase
Analyse Crystal structure of helicobacter pylori undecaprenyl pyrophosphate synthase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2D2R
- Type
- protein
- Length
- 418 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Undecaprenyl pyrophosphate synthase
- EC
- 2.5.1.31
- UniProt
- P55984
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Undecaprenyl pyrophosphate synthase (EC 2.5.1.31) | protein | 215 | 48% helix, 13% strand | P55984 |
| B | Undecaprenyl pyrophosphate synthase (EC 2.5.1.31) | protein | 203 | 51% helix, 14% strand | P55984 |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 369 | 0.65 | 0.79 | 27 | empty |
| 2 | 331 | 0.64 | 0.79 | 29 | empty |
| 3 | 103 | 0.32 | 0.72 | 17 | empty |
| 4 | 73 | 0.29 | 0.73 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1730 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 2D2R · Crystal structure of Helicobacter pylori Undecaprenyl Pyrophosphate Synthase · the same entry in another collection · chain A against A, TM-score 1.00
- P55984 · AlphaFold monomer V2.0 prediction for isoprenyl transferase (P55984) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P55984
- Elsewhere: RCSB PDB 2D2R · PDBe 2D2R · UniProt P55984
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