MolNFT v1 · #79637 · protein
Crystal structure of 5'-deoxy-5'-methylthioadenosine phosphorylase (mtap) II complexed with 5'-deoxy-5'-methylthioadenosine and sulfate
3T94: “Crystal structure of 5'-deoxy-5'-methylthioadenosine phosphorylase (mtap) II complexed with…”. X-ray diffraction, 2 ligands (MTA, SO4), 14 pockets (best druggability 0.79). MolNFT v1 #79637 on GenesisL1: 3D structure, binding sites…
- PDB
- 3T94
- Type
- protein
- Length
- 1,620 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-methylthioadenosine phosphorylase (mtap)
- EC
- 2.4.2.28
- UniProt
- Q97W94
- Ligands
- MTA, SO4
- Pockets
- 14 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 30% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | 5'-methylthioadenosine phosphorylase (mtap) (EC 2.4.2.28) | protein | 270 | 30% helix, 23% strand | Q97W94 |
Ligands and binding sites
- MTA · 5'-deoxy-5'-methylthioadenosine · ligand · 6 copies · chains A, B, C, D, E, F
- SO4 · Sulfate ion · ion · 11 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 124 | 0.79 | 0.97 | 28 | MTA, SO4 |
| 2 | 124 | 0.79 | 0.97 | 28 | MTA, SO4 |
| 3 | 123 | 0.78 | 0.97 | 27 | MTA, SO4 |
| 4 | 122 | 0.77 | 0.96 | 29 | MTA, SO4 |
| 5 | 118 | 0.77 | 0.96 | 28 | MTA, SO4 |
Interfaces
6 interfaces between chains.
- A–C · 1339 Ų buried · 22 hydrogen bonds · protein-protein
- B–C · 1308 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 1302 Ų buried · 19 hydrogen bonds · protein-protein
- D–F · 1289 Ų buried · 21 hydrogen bonds · protein-protein
- E–F · 1274 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 3T94 · Crystal structure of 5'-deoxy-5'-methylthioadenosine phosphorylase (MTAP) II complexed… · the same entry in another collection · chain C against C, TM-score 1.00
- Q97W94 · AlphaFold monomer V2.0 prediction for S-methyl-5'-thioadenosine phosphorylase (Q97W94) · 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 Q97W94
- Elsewhere: RCSB PDB 3T94 · PDBe 3T94 · UniProt Q97W94
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