Research workbench
Crystal structure of DddY mutant Y260A
Analyse Crystal structure of DddY mutant Y260A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Y4K
- Type
- protein
- Length
- 380 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2
- Source
- Acinetobacter bereziniae NIPH 3
- Molecule
- DMSP lyase DddY
- UniProt
- N8X9V6
- Ligands
- AKR, ZN
- Pockets
- 3 · best druggability 0.62
Structure
x-ray diffraction · resolution 2 · 1 distinct chain · 29% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DMSP lyase DddY | protein | 380 | 29% helix, 26% strand | N8X9V6 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 187 | 0.62 | 0.82 | 34 | ZN, AKR |
| 2 | 58 | 0.30 | 0.75 | 15 | empty |
| 3 | 61 | 0.30 | 0.74 | 17 | empty |
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5Y4K · Crystal structure of dddy mutant Y260A · 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 N8X9V6
- Elsewhere: RCSB PDB 5Y4K · PDBe 5Y4K · UniProt N8X9V6
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