Research workbench
Crystal structure of a putative methylthioadenosine nucleosidase from weissella paramesenteroides atcc 33313 (target nysgrc-029342 )
Analyse Crystal structure of a putative methylthioadenosine nucleosidase from weissella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KN5
- Type
- protein
- Length
- 461 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Methylthioadenosine nucleosidase
- EC
- 3.2.2.16
- UniProt
- C5RAK4
- Pockets
- 5 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Methylthioadenosine nucleosidase (EC 3.2.2.16) | protein | 235 | 36% helix, 29% strand | C5RAK4 |
| B | Methylthioadenosine nucleosidase (EC 3.2.2.16) | protein | 226 | 35% helix, 31% strand | C5RAK4 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 296 | 0.59 | 0.78 | 34 | EDO |
| 2 | 268 | 0.57 | 0.78 | 25 | empty |
| 3 | 256 | 0.54 | 0.76 | 38 | empty |
| 4 | 63 | 0.40 | 0.80 | 15 | empty |
| 5 | 52 | 0.38 | 0.80 | 15 | EDO |
Interfaces
1 interface between chains.
- A–B · 1357 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 modified (engineered).
Compared structures
- 4KN5 · Crystal structure of a putative methylthioadenosine nucleosidase from Weissella… · 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 C5RAK4
- Elsewhere: RCSB PDB 4KN5 · PDBe 4KN5 · UniProt C5RAK4
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