Research workbench
Crystal structure of 5'-deoxy-5'-methylthioadenosine phosphorylase in complex with a transition state analogue
Analyse Crystal structure of 5'-deoxy-5'-methylthioadenosine phosphorylase in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1K27
- Type
- protein
- Length
- 270 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-deoxy-5'-methylthioadenosine phosphorylase
- EC
- 2.4.2.28
- UniProt
- Q13126
- Ligands
- MTM, PO4
- Pockets
- 3 · best druggability 0.66
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-deoxy-5'-methylthioadenosine phosphorylase (EC 2.4.2.28) | protein | 270 | 32% helix, 26% strand | Q13126 |
Ligands and binding sites
- MTM · (3S,4R)-2-(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)-5-[(methylsulfanyl)methyl]pyrrolidine-3,4-diol · ligand · chains A
- PO4 · Phosphate ion · ion · 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 | 183 | 0.66 | 0.85 | 26 | PO4, MTM |
| 2 | 129 | 0.42 | 0.75 | 20 | empty |
| 3 | 51 | 0.32 | 0.77 | 15 | empty |
Compared structures
- 1K27 · Crystal Structure of 5'-Deoxy-5'-Methylthioadenosine Phosphorylase in Complex with a… · 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 1K27 · PDBe 1K27 · UniProt Q13126
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