MolNFT v1 · #11141 · protein
5'-deoxy-5'-methylthioadenosine phosphorylase complex with phosphate (space group P21)
1JDS: “5'-deoxy-5'-methylthioadenosine phosphorylase complex with phosphate (space group P21)”. X-ray diffraction, 1 ligand (PO4), 20 pockets (best druggability 0.79). MolNFT v1 #11141 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 1JDS
- Type
- protein
- Length
- 1,368 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
- PO4
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 3 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 | 226 | 35% helix, 31% strand | P50389 |
| C | 5'-methylthioadenosine phosphorylase (EC 2.4.2.28) | protein | 234 | 35% helix, 29% strand | P50389 |
| F | 5'-methylthioadenosine phosphorylase (EC 2.4.2.28) | protein | 230 | 36% helix, 30% strand | P50389 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 6 copies · chains A, D, B, C, E, F
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 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 | 569 | 0.79 | 0.86 | 57 | empty |
| 2 | 532 | 0.70 | 0.79 | 48 | PO4, TRS |
| 3 | 55 | 0.67 | 0.96 | 21 | empty |
| 4 | 253 | 0.67 | 0.84 | 39 | PO4, TRS |
| 5 | 54 | 0.67 | 0.96 | 19 | empty |
Interfaces
12 interfaces between chains.
- B–C · 1649 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 1603 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 1593 Ų buried · 12 hydrogen bonds · protein-protein
- B–E · 1150 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 1134 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1JDS · 5'-deoxy-5'-methylthioadenosine phosphorylase complex with phosphate (space group P21) · 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 F 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 1JDS · PDBe 1JDS · UniProt P50389
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