MolNFT v1 · #152361 · protein
Aeromonas hydrophila mtan-2 complexed with adenine
6IF8 · 5'-METHYLTHIOADENOSINE/S-adenosylhomocysteine nucleosidase: “Aeromonas hydrophila mtan-2 complexed with adenine”. X-ray diffraction, 1 ligand (ADE), 7 pockets (best druggability 0.79). MolNFT v1 #152361 on GenesisL1: 3D structure…
- PDB
- 6IF8
- Type
- protein
- Length
- 910 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
- A0KIZ1
- Ligands
- ADE
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | 5'-METHYLTHIOADENOSINE/S-adenosylhomocysteine nucleosidase (EC 3.2.2.9) | protein | 227 | 37% helix, 33% strand | A0KIZ1 |
| B, D | 5'-METHYLTHIOADENOSINE/S-adenosylhomocysteine nucleosidase (EC 3.2.2.9) | protein | 228 | 36% helix, 32% strand | A0KIZ1 |
Ligands and binding sites
- ADE · Adenine · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1152 | 0.79 | 0.81 | 95 | empty |
| 2 | 67 | 0.74 | 0.99 | 22 | ADE |
| 3 | 58 | 0.74 | 0.99 | 20 | ADE |
| 4 | 133 | 0.70 | 0.90 | 28 | ADE |
| 5 | 134 | 0.69 | 0.90 | 27 | ADE |
Interfaces
5 interfaces between chains.
- C–D · 1627 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1609 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 690 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 201 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 198 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
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 A0KIZ1
- Elsewhere: RCSB PDB 6IF8 · PDBe 6IF8 · UniProt A0KIZ1
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