Research workbench
Crystal structure of vibrio cholerae 5'-METHYLTHIOADENOSINE/S-adenosyl homocysteine nucleosidase (mtan) complexed with methylthio-dadme- immucillin-a
Analyse Crystal structure of vibrio cholerae 5'-METHYLTHIOADENOSINE/S-adenosyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WKB
- Type
- protein
- Length
- 474 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-METHYLTHIOADENOSINE/S-adenosylhomocysteine nucleosidase
- EC
- 3.2.2.9
- UniProt
- A5F5R2
- Ligands
- TDI
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 5'-METHYLTHIOADENOSINE/S-adenosylhomocysteine nucleosidase (EC 3.2.2.9) | protein | 237 | 38% helix, 31% strand | A5F5R2 |
Ligands and binding sites
- TDI · (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl) methyl]-4-[(methylsulfanyl)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
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 107 | 0.72 | 0.93 | 23 | TDI |
| 2 | 120 | 0.72 | 0.92 | 25 | TDI |
| 3 | 252 | 0.55 | 0.77 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 1422 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4WKB · Crystal structure of Vibrio cholerae 5'-methylthioadenosine/S-adenosyl homocysteine… · the same entry in another collection · chain A against A, TM-score 1.00
- A5F5R2 · AlphaFold monomer V2.0 prediction for 5'-METHYLTHIOADENOSINE/S-adenosylhomocysteine… · a predicted model of the same protein · chain A against A, TM-score 0.96
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 A5F5R2
- Elsewhere: RCSB PDB 4WKB · PDBe 4WKB · UniProt A5F5R2
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