Research workbench
A. thaliana mta nucleosidase in complex with S-adenosylhomocysteine
Analyse A. thaliana mta nucleosidase in complex with S-adenosylhomocysteine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LGS
- Type
- protein
- Length
- 983 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-methylthioadenosine nucleosidases
- EC
- 3.2.2.16
- UniProt
- Q9T0I8
- Ligands
- SAH, ADE
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-methylthioadenosine nucleosidases (EC 3.2.2.16) | protein | 246 | 37% helix, 26% strand | Q9T0I8 |
| B, D | 5'-methylthioadenosine nucleosidases (EC 3.2.2.16) | protein | 245 | 37% helix, 26% strand | Q9T0I8 |
| C | 5'-methylthioadenosine nucleosidases (EC 3.2.2.16) | protein | 247 | 37% helix, 26% strand | Q9T0I8 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · 4 copies · chains A, B, C, D
- ADE · Adenine · ligand · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 97 | 0.76 | 0.97 | 24 | SAH, ADE |
| 2 | 90 | 0.76 | 0.97 | 25 | SAH, ADE |
| 3 | 94 | 0.75 | 0.96 | 23 | SAH, ADE |
| 4 | 95 | 0.75 | 0.96 | 25 | SAH, ADE |
| 5 | 572 | 0.70 | 0.79 | 78 | empty |
Interfaces
6 interfaces between chains.
- C–D · 2126 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 2047 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 375 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 151 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 140 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3LGS · A. thaliana MTA nucleosidase in complex with S-adenosylhomocysteine · 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 C 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 3LGS · PDBe 3LGS · UniProt Q9T0I8
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