Research workbench
Crystal structure of H. pylori referent strain in complex with PO4
Analyse Crystal structure of H. pylori referent strain in complex with PO4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LU0
- Type
- protein
- Length
- 1,398 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Purine nucleoside phosphorylase deod-type
- EC
- 2.4.2.1
- UniProt
- I9S9Z7
- Ligands
- PO4
- Pockets
- 13 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Purine nucleoside phosphorylase deod-type (EC 2.4.2.1) | protein | 233 | 35% helix, 29% strand | I9S9Z7 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 4 copies · chains A, D, B, E, C, F
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, D, B, E, C, F
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 4 copies · chains A, D, B, E, C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 848 | 0.75 | 0.79 | 72 | empty |
| 2 | 358 | 0.70 | 0.82 | 44 | PO4, TRS |
| 3 | 381 | 0.69 | 0.81 | 49 | empty |
| 4 | 216 | 0.68 | 0.86 | 50 | PO4, TRS, EDO |
| 5 | 377 | 0.67 | 0.80 | 49 | empty |
Interfaces
12 interfaces between chains.
- B–D · 1855 Ų buried · 34 hydrogen bonds · protein-protein
- B–E · 1836 Ų buried · 6 hydrogen bonds · protein-protein
- C–E · 1835 Ų buried · 34 hydrogen bonds · protein-protein
- A–F · 1831 Ų buried · 34 hydrogen bonds · protein-protein
- C–F · 1817 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5LU0 · Crystal structure of H. pylori referent strain in complex with PO4 · 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 I9S9Z7
- Elsewhere: RCSB PDB 5LU0 · PDBe 5LU0 · UniProt I9S9Z7
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