MolNFT v1 · #134682 · protein
Crystal structure of human 5'-deoxy-5'-methylthioadenosine phosphorylase in complex with methylthio-dadme-immucillin-a
5TC8 · S-methyl-5'-thioadenosine phosphorylase: “Crystal structure of human 5'-deoxy-5'-methylthioadenosine phosphorylase in complex with…”. X-ray diffraction, 4 ligands (TDI, MG, PO4), 3 pockets (best druggability 0.67). MolNFT v1 #134682…
- PDB
- 5TC8
- Type
- protein
- Length
- 273 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- S-methyl-5'-thioadenosine phosphorylase
- EC
- 2.4.2.28
- UniProt
- Q13126
- Ligands
- TDI, MG, PO4, CL
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | S-methyl-5'-thioadenosine phosphorylase (EC 2.4.2.28) | protein | 273 | 32% helix, 24% strand | Q13126 |
Ligands and binding sites
- TDI · (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl) methyl]-4-[(methylsulfanyl)methyl]pyrrolidin-3-ol · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- PO4 · Phosphate ion · ion · chains A
- CL · Chloride ion · ion · chains A
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A
- 2PE · Nonaethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 195 | 0.67 | 0.85 | 28 | TDI, PO4 |
| 2 | 91 | 0.39 | 0.76 | 16 | PEG |
| 3 | 51 | 0.34 | 0.78 | 20 | empty |
Compared structures
- 5TC8 · Crystal structure of human 5'-deoxy-5'-methylthioadenosine phosphorylase in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q13126 · AlphaFold monomer V2.0 prediction for S-methyl-5'-thioadenosine phosphorylase (Q13126) · 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 Q13126
- Elsewhere: RCSB PDB 5TC8 · PDBe 5TC8 · UniProt Q13126
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