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-butyl-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
- 6DYY
- Type
- protein
- Length
- 924 residues
- Chains
- 4
- 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
- OS6, MG
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | 5'-METHYLTHIOADENOSINE/S-adenosylhomocysteine nucleosidase (EC 3.2.2.9) | protein | 232 | 38% helix, 31% strand | A0A1W0VQJ9 |
| B, C | 5'-METHYLTHIOADENOSINE/S-adenosylhomocysteine nucleosidase (EC 3.2.2.9) | protein | 230 | 39% helix, 31% strand | A0A1W0VQJ9 |
Ligands and binding sites
- OS6 · (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl) methyl]-4-({[3-(1-butyl-1H-1,2,3-triazol-4-yl) propyl]sulfanyl}methyl)pyrrolidin-3-ol · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 2 copies · chains A, B, D
- EDO · 1,2-ethanediol · additive · 7 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1153 | 0.79 | 0.81 | 99 | EDO, OS6 |
| 2 | 142 | 0.72 | 0.91 | 30 | OS6 |
| 3 | 86 | 0.61 | 0.88 | 19 | OS6 |
| 4 | 198 | 0.61 | 0.82 | 33 | OS6 |
| 5 | 186 | 0.45 | 0.74 | 24 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1696 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 332 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 297 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 97 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6DYY · Crystal structure of Helicobacter pylori 5'-methylthioadenosine/S-adenosyl homocysteine… · the same entry in another collection · chain D against D, 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 6DYY · PDBe 6DYY · UniProt A0A1W0VQJ9
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