Research workbench
Crystal structure of 5'-deoxy-5'-methylthioadenosine phosphorylase complexed with SO4
Analyse Crystal structure of 5'-deoxy-5'-methylthioadenosine phosphorylase complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JPV
- Type
- protein
- Length
- 703 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-deoxy-5'-methylthioadenosine phosphorylase
- EC
- 2.4.2.28
- UniProt
- P50389
- Ligands
- SO4
- Pockets
- 13 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-deoxy-5'-methylthioadenosine phosphorylase (EC 2.4.2.28) | protein | 235 | 34% helix, 29% strand | P50389 |
| B, C | 5'-deoxy-5'-methylthioadenosine phosphorylase (EC 2.4.2.28) | protein | 234 | 35% helix, 29% strand | P50389 |
Ligands and binding sites
- 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
13 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 56 | 0.67 | 0.96 | 19 | empty |
| 2 | 52 | 0.67 | 0.96 | 16 | empty |
| 3 | 340 | 0.65 | 0.80 | 39 | SO4 |
| 4 | 386 | 0.65 | 0.79 | 42 | SO4 |
| 5 | 200 | 0.48 | 0.75 | 25 | SO4 |
Interfaces
3 interfaces between chains.
- B–C · 1580 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 1144 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 47 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1JPV · Crystal Structure of 5'-deoxy-5'-methylthioadenosine phosphorylase complexed with SO4 · the same entry in another collection · chain A against A, TM-score 1.00
- P50389 · AlphaFold monomer V2.0 prediction for purine nucleoside phosphorylase (P50389) · 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 P50389
- Elsewhere: RCSB PDB 1JPV · PDBe 1JPV · UniProt P50389
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