MolNFT v1 · #49622 · protein
Crystal structure of arabidopsis thaliana 5'-methylthioadenosine nucleosidase in complex with formycin a
2QTT: “Crystal structure of arabidopsis thaliana 5'-methylthioadenosine nucleosidase in complex with formycin a”. X-ray diffraction, 2 ligands (ADE, FMC), 3 pockets (best druggability 0.74). MolNFT v1 #49622 on GenesisL1: 3D structure…
- PDB
- 2QTT
- Type
- protein
- Length
- 493 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-methylthioadenosine nucleosidase
- EC
- 3.2.2.16
- UniProt
- Q9T0I8
- Ligands
- ADE, FMC
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-methylthioadenosine nucleosidase (EC 3.2.2.16) | protein | 248 | 36% helix, 25% strand | Q9T0I8 |
| B | 5'-methylthioadenosine nucleosidase (EC 3.2.2.16) | protein | 245 | 37% helix, 26% strand | Q9T0I8 |
Ligands and binding sites
- ADE · Adenine · ligand · chains A
- FMC · (1S)-1-(7-amino-1H-pyrazolo[4,3-d]pyrimidin-3-yl)-1,4-anhydro-D-ribitol · ligand · chains B
- EDO · 1,2-ethanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 93 | 0.74 | 0.95 | 27 | FMC |
| 2 | 374 | 0.67 | 0.80 | 39 | ADE |
| 3 | 56 | 0.29 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 2016 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 2QTT · Crystal Structure of Arabidopsis thaliana 5'-Methylthioadenosine nucleosidase in complex… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9T0I8 · AlphaFold monomer V2.0 prediction for 5'-methylthioadenosine nucleosidase (Q9T0I8) · a predicted model of the same protein · chain B 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 Q9T0I8
- Elsewhere: RCSB PDB 2QTT · PDBe 2QTT · UniProt Q9T0I8
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