MolNFT v1 · #34870 · protein
Crystal structure of helicobacter pylori undecaprenyl pyrophosphate synthase complexed with pyrophosphate
2DTN: “Crystal structure of helicobacter pylori undecaprenyl pyrophosphate synthase complexed with pyrophosphate”. X-ray diffraction, 1 ligand (DPO), 4 pockets (best druggability 0.63). MolNFT v1 #34870 on GenesisL1: 3D structure, binding…
- PDB
- 2DTN
- Type
- protein
- Length
- 417 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
- Ligands
- DPO
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Undecaprenyl pyrophosphate synthase (EC 2.5.1.31) | protein | 214 | 49% helix, 13% strand | P55984 |
| B | Undecaprenyl pyrophosphate synthase (EC 2.5.1.31) | protein | 203 | 48% helix, 15% strand | P55984 |
Ligands and binding sites
- DPO · Diphosphate · ligand · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 359 | 0.63 | 0.78 | 34 | empty |
| 2 | 228 | 0.58 | 0.79 | 23 | empty |
| 3 | 98 | 0.31 | 0.72 | 17 | empty |
| 4 | 79 | 0.28 | 0.72 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1617 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 2DTN · Crystal structure of Helicobacter pylori undecaprenyl pyrophosphate synthase complexed… · 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 2DTN · PDBe 2DTN · UniProt P55984
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