MolNFT v1 · #135942 · protein
Crystal structure of 5'-METHYLTHIOADENOSINE/S-adenosylhomocysteine nucleosidase in complex with adenine from vibrio fischeri ES114
5UE1: “Crystal structure of 5'-METHYLTHIOADENOSINE/S-adenosylhomocysteine nucleosidase in complex with adenine from…”. X-ray diffraction, 3 ligands (9DA, CA, CL), 3 pockets (best druggability 0.70). MolNFT v1 #135942 on GenesisL1: 3D…
- PDB
- 5UE1
- Type
- protein
- Length
- 466 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
- Q5E2X3
- Ligands
- 9DA, CA, CL
- Pockets
- 3 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 5'-METHYLTHIOADENOSINE/S-adenosylhomocysteine nucleosidase (EC 3.2.2.9) | protein | 233 | 36% helix, 32% strand | Q5E2X3 |
Ligands and binding sites
- 9DA · 9-deazaadenine · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 3 copies · chains A
- CL · Chloride ion · ion · 5 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 127 | 0.70 | 0.90 | 24 | 9DA, TRS, EDO |
| 2 | 130 | 0.68 | 0.89 | 26 | 9DA, TRS |
| 3 | 159 | 0.49 | 0.78 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 1554 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5UE1 · Crystal structure of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase in… · the same entry in another collection · chain A against A, TM-score 1.00
- Q5E2X3 · AlphaFold monomer V2.0 prediction for 5'-METHYLTHIOADENOSINE/S-adenosylhomocysteine… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q5E2X3
- Elsewhere: RCSB PDB 5UE1 · PDBe 5UE1 · UniProt Q5E2X3
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