Research workbench
Crystal structure of helicobacter pylori 5'-METHYLTHIOADENOSINE/S- adenosyl homocysteine nucleosidase (mtan) complexed with (3R,4S)-1- ((4-amino-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL)-4-(((3-(1-benzyl- 1H-1,2,3-triazol-4-YL)PROPYL)THIO)METHYL)PYRROLIDIN-3-ol
Analyse Crystal structure of helicobacter pylori 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
- 6DYW
- Type
- protein
- Length
- 464 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
- A0A1W0VQJ9
- Ligands
- OS5, NH4
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 5'-METHYLTHIOADENOSINE/S-adenosylhomocysteine nucleosidase (EC 3.2.2.9) | protein | 232 | 38% helix, 30% strand | A0A1W0VQJ9 |
Ligands and binding sites
- OS5 · (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl) methyl]-4-({[3-(1-benzyl-1H-1,2,3-triazol-4-yl) propyl]sulfanyl}methyl)pyrrolidin-3-ol · ligand · 2 copies · chains A, B
- NH4 · Ammonium ion · ion · chains B
- EDO · 1,2-ethanediol · additive · 12 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 | 834 | 0.71 | 0.76 | 73 | EDO |
| 2 | 88 | 0.63 | 0.89 | 19 | OS5 |
| 3 | 109 | 0.62 | 0.87 | 19 | OS5 |
Interfaces
1 interface between chains.
- A–B · 313 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6DYW · Crystal structure of Helicobacter pylori 5'-methylthioadenosine/S-adenosyl homocysteine… · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A1W0VQJ9
- Elsewhere: RCSB PDB 6DYW · PDBe 6DYW · UniProt A0A1W0VQJ9
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