Research workbench
Crystal structure of K. pneumoniae MTA/ADOHCY nucleosidase in complex with fragmented S-adenosyl-L-homocysteine
Analyse Crystal structure of K. pneumoniae MTA/ADOHCY nucleosidase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4G89
- 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
- A6T4W3
- Ligands
- ADE, SAH, SO4
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 5'-METHYLTHIOADENOSINE/S-adenosylhomocysteine nucleosidase (EC 3.2.2.9) | protein | 233 | 39% helix, 31% strand | A6T4W3 |
Ligands and binding sites
- ADE · Adenine · ligand · chains A
- SAH · S-adenosyl-L-homocysteine · ligand · chains A, B
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 108 | 0.68 | 0.90 | 23 | ADE, SAH |
| 2 | 328 | 0.64 | 0.79 | 37 | empty |
| 3 | 284 | 0.62 | 0.80 | 33 | empty |
| 4 | 72 | 0.50 | 0.84 | 23 | empty |
| 5 | 96 | 0.37 | 0.75 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1362 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4G89 · Crystal structure of k. pneumoniae mta/adohcy nucleosidase in complex with fragmented… · the same entry in another collection · chain A against A, TM-score 1.00
- A6T4W3 · 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 A6T4W3
- Elsewhere: RCSB PDB 4G89 · PDBe 4G89 · UniProt A6T4W3
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