MolNFT v1 · #116651 · protein
Crystal structure of a 5'-METHYLTHIOADENOSINE/S-adenosylhomocysteine (MTA/SAH) nucleosidase (mtan) from colwellia psychrerythraea 34H (CPS_4743, target psi-029300) in complex with adenine at 2.27 a resolution
5DK6 · 5'-METHYLTHIOADENOSINE/S-adenosylhomocysteine nucleosidase: “Crystal structure of a 5'-METHYLTHIOADENOSINE/S-adenosylhomocysteine (MTA/SAH) nucleosidase (mtan) from…”. X-ray diffraction, 2 ligands (GLY, ADE), 1 pocket (best…
- PDB
- 5DK6
- Type
- protein
- Length
- 242 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-METHYLTHIOADENOSINE/S-adenosylhomocysteine nucleosidase
- EC
- 3.2.2.9
- UniProt
- Q47UY5
- Ligands
- GLY, ADE
- Pockets
- 1 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5'-METHYLTHIOADENOSINE/S-adenosylhomocysteine nucleosidase (EC 3.2.2.9) | protein | 242 | 34% helix, 29% strand | Q47UY5 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 86 | 0.63 | 0.90 | 20 | GLY, ADE |
Modifications
Observed in the structure: 7 modified (engineered).
Compared structures
- 5DK6 · Crystal structure of a 5'-METHYLTHIOADENOSINE/S-adenosylhomocysteine (MTA/SAH)… · the same entry in another collection · chain A against A, TM-score 1.00
- Q47UY5 · AlphaFold monomer V2.0 prediction for 5'-METHYLTHIOADENOSINE/S-adenosylhomocysteine… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q47UY5
- Elsewhere: RCSB PDB 5DK6 · PDBe 5DK6 · UniProt Q47UY5
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