MolNFT v1 · #74528 · protein
Crystal structure of human 5'-deoxy-5'-methyladenosine phosphorylase
3OZE · S-methyl-5'-thioadenosine phosphorylase: “Crystal structure of human 5'-deoxy-5'-methyladenosine phosphorylase”. X-ray diffraction, 1 ligand (PO4), 19 pockets (best druggability 0.77). MolNFT v1 #74528 on GenesisL1: 3D structure…
- PDB
- 3OZE
- Type
- protein
- Length
- 1,584 residues
- Chains
- 6
- 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
- PO4
- Pockets
- 19 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 31% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | S-methyl-5'-thioadenosine phosphorylase (EC 2.4.2.28) | protein | 263 | 31% helix, 27% strand | Q13126 |
| B | S-methyl-5'-thioadenosine phosphorylase (EC 2.4.2.28) | protein | 268 | 30% helix, 26% strand | Q13126 |
| C | S-methyl-5'-thioadenosine phosphorylase (EC 2.4.2.28) | protein | 261 | 32% helix, 27% strand | Q13126 |
| E | S-methyl-5'-thioadenosine phosphorylase (EC 2.4.2.28) | protein | 264 | 31% helix, 27% strand | Q13126 |
| F | S-methyl-5'-thioadenosine phosphorylase (EC 2.4.2.28) | protein | 265 | 31% helix, 26% strand | Q13126 |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 304 | 0.77 | 0.89 | 72 | empty |
| 2 | 337 | 0.76 | 0.87 | 72 | empty |
| 3 | 520 | 0.72 | 0.81 | 43 | PO4 |
| 4 | 471 | 0.70 | 0.80 | 39 | PO4 |
| 5 | 426 | 0.69 | 0.81 | 38 | PO4 |
Interfaces
7 interfaces between chains.
- E–F · 1042 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1037 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1007 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 985 Ų buried · 12 hydrogen bonds · protein-protein
- D–F · 979 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 3OZE · Crystal Structure of human 5'-deoxy-5'-methyladenosine phosphorylase · the same entry in another collection · chain F against F, 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 E 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 3OZE · PDBe 3OZE · UniProt Q13126
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