MolNFT v1 · #74527 · protein
Crystal structure of human 5'-deoxy-5'-methyladenosine phosphorylase in complex with pcl-phenylthiodadmeimma
3OZD · S-methyl-5'-thioadenosine phosphorylase: “Crystal structure of human 5'-deoxy-5'-methyladenosine phosphorylase in complex with pcl-phenylthiodadmeimma”. X-ray diffraction, 1 ligand (4CT), 6 pockets (best druggability 0.72). MolNFT…
- PDB
- 3OZD
- Type
- protein
- Length
- 546 residues
- Chains
- 2
- 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
- 4CT
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 31% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | S-methyl-5'-thioadenosine phosphorylase (EC 2.4.2.28) | protein | 273 | 31% helix, 25% strand | Q13126 |
Ligands and binding sites
- 4CT · (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl) methyl]-4-{[(4-chlorophenyl) sulfanyl]methyl}pyrrolidin-3-ol · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 731 | 0.72 | 0.78 | 78 | 4CT |
| 2 | 632 | 0.71 | 0.79 | 80 | 4CT |
| 3 | 71 | 0.32 | 0.75 | 18 | empty |
| 4 | 64 | 0.31 | 0.75 | 14 | empty |
| 5 | 65 | 0.30 | 0.74 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 669 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3OZD · Crystal Structure of human 5'-deoxy-5'-methyladenosine 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 0.97
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 3OZD · PDBe 3OZD · UniProt Q13126
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.