Research workbench
Crystal structure of 5'-deoxy-5'-methylthioadenosine phosphorylase complexed with adenosine and sulfate ion
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
- 1JDV
- Type
- protein
- Length
- 1,378 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-methylthioadenosine phosphorylase
- EC
- 2.4.2.28
- UniProt
- P50389
- Ligands
- ADN, SO4
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D, E | 5'-methylthioadenosine phosphorylase (EC 2.4.2.28) | protein | 227 | 37% helix, 31% strand | P50389 |
| C, F | 5'-methylthioadenosine phosphorylase (EC 2.4.2.28) | protein | 235 | 34% helix, 29% strand | P50389 |
Ligands and binding sites
- ADN · Adenosine · ligand · 4 copies · chains A, D, B, C, E, F
- SO4 · Sulfate ion · ion · 6 copies · chains A, D, B, C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 961 | 0.81 | 0.83 | 89 | empty |
| 2 | 55 | 0.71 | 0.98 | 20 | empty |
| 3 | 56 | 0.70 | 0.97 | 23 | empty |
| 4 | 57 | 0.68 | 0.96 | 17 | empty |
| 5 | 442 | 0.68 | 0.79 | 49 | SO4 |
Interfaces
12 interfaces between chains.
- B–C · 1611 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 1599 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 1549 Ų buried · 12 hydrogen bonds · protein-protein
- B–E · 1187 Ų buried · 21 hydrogen bonds · protein-protein
- D–F · 1150 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1JDV · Crystal structure of 5'-deoxy-5'-methylthioadenosine phosphorylase complexed with… · the same entry in another collection · chain F against F, 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 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 P50389
- Elsewhere: RCSB PDB 1JDV · PDBe 1JDV · UniProt P50389
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