MolNFT v1 · #11143 · protein
Crystal structure of 5'-deoxy-5'-methylthioadenosine phosphorylase
1JDU: “Crystal structure of 5'-deoxy-5'-methylthioadenosine phosphorylase”. X-ray diffraction, 11 pockets (best druggability 0.72). MolNFT v1 #11143 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1JDU
- Type
- protein
- Length
- 694 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
- Pockets
- 11 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-methylthioadenosine phosphorylase (EC 2.4.2.28) | protein | 231 | 35% helix, 29% strand | P50389 |
| B | 5'-methylthioadenosine phosphorylase (EC 2.4.2.28) | protein | 229 | 35% helix, 29% strand | P50389 |
| C | 5'-methylthioadenosine phosphorylase (EC 2.4.2.28) | protein | 234 | 35% helix, 29% strand | P50389 |
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.72 | 0.99 | 23 | empty |
| 2 | 430 | 0.68 | 0.80 | 51 | empty |
| 3 | 395 | 0.66 | 0.79 | 42 | empty |
| 4 | 52 | 0.65 | 0.95 | 21 | empty |
| 5 | 252 | 0.52 | 0.75 | 35 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1636 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 1130 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 46 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 1JDU · Crystal structure of 5'-deoxy-5'-methylthioadenosine phosphorylase · the same entry in another collection · chain B against B, TM-score 1.00
- P50389 · AlphaFold monomer V2.0 prediction for purine nucleoside phosphorylase (P50389) · a predicted model of the same protein · chain B 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 1JDU · PDBe 1JDU · UniProt P50389
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