Research workbench
Crystal structure of 5'-deoxy-5'-methylthioadenosine phosphorylase with formycin B and sulfate ion
Analyse Crystal structure of 5'-deoxy-5'-methylthioadenosine phosphorylase with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JDZ
- Type
- protein
- Length
- 678 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-methylthioadenosine phosphorylase
- EC
- 2.4.2.28
- UniProt
- P50389
- Ligands
- FMB, SO4
- Pockets
- 13 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | 5'-methylthioadenosine phosphorylase (EC 2.4.2.28) | protein | 226 | 35% helix, 31% strand | P50389 |
Ligands and binding sites
- FMB · Formycin B · 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
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 69 | 0.75 | 0.99 | 30 | empty |
| 2 | 57 | 0.68 | 0.96 | 20 | empty |
| 3 | 58 | 0.68 | 0.96 | 17 | empty |
| 4 | 359 | 0.65 | 0.80 | 48 | SO4, FMB |
| 5 | 312 | 0.64 | 0.80 | 38 | SO4, FMB |
Interfaces
3 interfaces between chains.
- B–C · 1625 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 1130 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 49 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1JDZ · Crystal structure of 5'-deoxy-5'-methylthioadenosine phosphorylase with formycin B and… · 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 0.99
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 1JDZ · PDBe 1JDZ · UniProt P50389
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