MolNFT v1 · #31832 · protein
Crystal structure of quinolinic acid phosphoribosyltransferase from helicobacter pylori with phthalic acid
2B7P · Probable nicotinate-nucleotide pyrophosphorylase: “Crystal structure of quinolinic acid phosphoribosyltransferase from helicobacter pylori with phthalic acid”. X-ray diffraction, 2 ligands (PHT, SO4), 11 pockets (best druggability…
- PDB
- 2B7P
- Type
- protein
- Length
- 819 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable nicotinate-nucleotide pyrophosphorylase
- EC
- 2.4.2.19
- UniProt
- O25909
- Ligands
- PHT, SO4
- Pockets
- 11 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Probable nicotinate-nucleotide pyrophosphorylase (EC 2.4.2.19) | protein | 273 | 42% helix, 20% strand | O25909 |
Ligands and binding sites
- PHT · Phthalic acid · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 779 | 0.75 | 0.79 | 88 | empty |
| 2 | 417 | 0.68 | 0.80 | 50 | empty |
| 3 | 483 | 0.65 | 0.77 | 48 | empty |
| 4 | 233 | 0.54 | 0.77 | 24 | empty |
| 5 | 170 | 0.50 | 0.78 | 27 | SO4, PHT |
Interfaces
3 interfaces between chains.
- A–B · 395 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 364 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 324 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2B7P · Crystal structure of quinolinic acid phosphoribosyltransferase from Helicobacter pylori… · the same entry in another collection · chain A against A, TM-score 1.00
- O25909 · AlphaFold monomer V2.0 prediction for probable nicotinate-nucleotide pyrophosphorylase… · a predicted model of the same protein · chain A against A, TM-score 0.98
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 O25909
- Elsewhere: RCSB PDB 2B7P · PDBe 2B7P · UniProt O25909
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