Research workbench
Crystal structure of wild-type mall from bacillus subtilis with ts analogue 1-deoxynojirimycin
Analyse Crystal structure of wild-type mall from bacillus subtilis with ts analogue… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WCZ
- Type
- protein
- Length
- 1,110 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oligo-1,6-glucosidase 1
- EC
- 3.2.1.10
- UniProt
- O06994
- Ligands
- NOJ
- Pockets
- 6 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oligo-1,6-glucosidase 1 (EC 3.2.1.10) | protein | 556 | 34% helix, 18% strand | O06994 |
| B | Oligo-1,6-glucosidase 1 (EC 3.2.1.10) | protein | 554 | 34% helix, 18% strand | O06994 |
Ligands and binding sites
- NOJ · 1-deoxynojirimycin · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
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 | 580 | 0.78 | 0.84 | 59 | NOJ, GOL |
| 2 | 548 | 0.77 | 0.84 | 51 | NOJ |
| 3 | 589 | 0.68 | 0.77 | 69 | empty |
| 4 | 80 | 0.38 | 0.77 | 21 | empty |
| 5 | 89 | 0.36 | 0.76 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 374 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5WCZ · Crystal Structure of Wild-Type MalL from Bacillus subtilis with TS analogue… · the same entry in another collection · chain A against A, TM-score 1.00
- O06994 · AlphaFold monomer V2.0 prediction for oligo-1,6-glucosidase 1 (O06994) · a predicted model of the same protein · chain B 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 O06994
- Elsewhere: RCSB PDB 5WCZ · PDBe 5WCZ · UniProt O06994
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