Research workbench
Crystal structure of calf spleen purine nucleoside phosphorylase in a new space group with full trimer in the asymmetric unit
Analyse Crystal structure of calf spleen purine nucleoside phosphorylase in a new space… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1LV8
- Type
- protein
- Length
- 1,593 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Purine nucleoside phosphorylase
- EC
- 2.4.2.1
- UniProt
- P55859
- Ligands
- 9PP, CA
- Pockets
- 19 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 265 | 31% helix, 24% strand | P55859 |
| C | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 267 | 30% helix, 24% strand | P55859 |
| F | Purine nucleoside phosphorylase (EC 2.4.2.1) | protein | 266 | 31% helix, 24% strand | P55859 |
Ligands and binding sites
- 9PP · 2,6-diamino-(S)-9-[2-(phosphonomethoxy)propyl]purine · ligand · 6 copies · chains A, B, C, D, E, F
- CA · Calcium ion · metal · 6 copies · chains A, D, B, F, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 106 | 0.79 | 0.98 | 18 | empty |
| 2 | 101 | 0.78 | 0.98 | 19 | empty |
| 3 | 1196 | 0.72 | 0.76 | 125 | CA, 9PP |
| 4 | 1003 | 0.72 | 0.76 | 108 | CA, 9PP |
| 5 | 307 | 0.63 | 0.80 | 40 | 9PP |
Interfaces
12 interfaces between chains.
- E–F · 1017 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1010 Ų buried · 14 hydrogen bonds · protein-protein
- D–F · 1009 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 1002 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1002 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 1LV8 · Crystal structure of calf spleen purine nucleoside phosphorylase in a new space group… · the same entry in another collection · chain F against F, TM-score 1.00
- P55859 · AlphaFold monomer V2.0 prediction for purine nucleoside phosphorylase (P55859) · 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 P55859
- Elsewhere: RCSB PDB 1LV8 · PDBe 1LV8 · UniProt P55859
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