MolNFT v1 · #143412 · protein
Crystal structure of campylobacter jejuni 5'-METHYLTHIOADENOSINE/S- adenosyl homocysteine nucleosidase (mtan) complexed with pyrazinylthio-dadme-immucillin-a
6AYT · 5'-METHYLTHIOADENOSINE/S-adenosylhomocysteine nucleosidase: “Crystal structure of campylobacter jejuni 5'-METHYLTHIOADENOSINE/S- adenosyl homocysteine nucleosidase (mtan)…”. X-ray diffraction, 1 ligand (4EH), 8 pockets (best…
- PDB
- 6AYT
- Type
- protein
- Length
- 916 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
- A0A1E7P7U4
- Ligands
- 4EH
- Pockets
- 8 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | 5'-METHYLTHIOADENOSINE/S-adenosylhomocysteine nucleosidase (EC 3.2.2.9) | protein | 229 | 38% helix, 30% strand | A0A1E7P7U4 |
Ligands and binding sites
- 4EH · (3R,4S)-1-[(4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl) methyl]-4-[(pyrazin-2-ylsulfanyl)methyl]pyrrolidin-3-ol · ligand · 4 copies · chains A, D, B, C
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 867 | 0.85 | 0.87 | 121 | EDO, 4EH |
| 2 | 632 | 0.81 | 0.85 | 67 | 4EH |
| 3 | 186 | 0.70 | 0.87 | 29 | 4EH |
| 4 | 148 | 0.68 | 0.88 | 28 | 4EH |
| 5 | 80 | 0.61 | 0.89 | 32 | empty |
Interfaces
5 interfaces between chains.
- B–C · 1621 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 1619 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 292 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 188 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 181 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6AYT · 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 6AYT · PDBe 6AYT · UniProt A0A1E7P7U4
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