Research workbench
Crystal structure of campylobacter jejuni 5'-METHYLTHIOADENOSINE/S- adenosyl homocysteine nucleosidase (mtan) complexed with 5'-deoxy-5'- propyl-dadme-immucillin-a
Analyse Crystal structure of campylobacter jejuni 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
- 6AYO
- Type
- protein
- Length
- 458 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
- A0A1E7P7U4
- Ligands
- C1Y
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 5'-METHYLTHIOADENOSINE/S-adenosylhomocysteine nucleosidase (EC 3.2.2.9) | protein | 229 | 39% helix, 30% strand | A0A1E7P7U4 |
Ligands and binding sites
- C1Y · (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl) methyl]-4-propylpyrrolidin-3-ol · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 133 | 0.72 | 0.91 | 24 | C1Y |
| 2 | 152 | 0.71 | 0.90 | 28 | C1Y |
| 3 | 75 | 0.59 | 0.89 | 26 | EDO |
| 4 | 78 | 0.58 | 0.88 | 25 | EDO |
| 5 | 190 | 0.50 | 0.76 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1639 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 6AYO · Crystal structure of Campylobacter jejuni 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 A0A1E7P7U4
- Elsewhere: RCSB PDB 6AYO · PDBe 6AYO · UniProt A0A1E7P7U4
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