MolNFT v1 · #11150 · protein
5'-deoxy-5'-methylthioadenosine phosphorylase complex with guanosine and sulfate
1JE1: “5'-deoxy-5'-methylthioadenosine phosphorylase complex with guanosine and sulfate”. X-ray diffraction, 2 ligands (GMP, SO4), 20 pockets (best druggability 0.80). MolNFT v1 #11150 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 1JE1
- Type
- protein
- Length
- 1,393 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
- GMP, SO4
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 6 distinct chains · 37% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-methylthioadenosine phosphorylase (EC 2.4.2.28) | protein | 232 | 37% helix, 30% strand | P50389 |
| B | 5'-methylthioadenosine phosphorylase (EC 2.4.2.28) | protein | 231 | 38% helix, 30% strand | P50389 |
| C | 5'-methylthioadenosine phosphorylase (EC 2.4.2.28) | protein | 235 | 36% helix, 29% strand | P50389 |
| D | 5'-methylthioadenosine phosphorylase (EC 2.4.2.28) | protein | 231 | 36% helix, 30% strand | P50389 |
| E | 5'-methylthioadenosine phosphorylase (EC 2.4.2.28) | protein | 230 | 38% helix, 30% strand | P50389 |
| F | 5'-methylthioadenosine phosphorylase (EC 2.4.2.28) | protein | 234 | 36% helix, 29% strand | P50389 |
Ligands and binding sites
- GMP · Guanosine · ligand · 6 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1103 | 0.80 | 0.82 | 107 | empty |
| 2 | 53 | 0.70 | 0.98 | 23 | empty |
| 3 | 57 | 0.68 | 0.96 | 22 | empty |
| 4 | 56 | 0.67 | 0.95 | 19 | empty |
| 5 | 349 | 0.66 | 0.81 | 36 | SO4, GMP |
Interfaces
12 interfaces between chains.
- E–F · 1581 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 1554 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 1501 Ų buried · 12 hydrogen bonds · protein-protein
- B–E · 1186 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 1136 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1JE1 · 5'-deoxy-5'-methylthioadenosine phosphorylase complex with guanosine and sulfate · 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 D 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 1JE1 · PDBe 1JE1 · UniProt P50389
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