Research workbench
Alginate lyase A1-III Y246F complexed with tetrasaccharide
Analyse Alginate lyase A1-III Y246F complexed with tetrasaccharide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4F13
- Type
- protein
- Length
- 697 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alginate lyase
- EC
- 4.2.2.3
- UniProt
- Q9KWU1
- Ligands
- MAW, BEM
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 57% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alginate lyase (EC 4.2.2.3) | protein | 352 | 57% helix, 2% strand | Q9KWU1 |
| B | Alginate lyase (EC 4.2.2.3) | protein | 345 | 57% helix, 2% strand | Q9KWU1 |
Ligands and binding sites
- MAW · 4-deoxy-alpha-L-erythro-hex-4-enopyranuronic acid · ligand · chains A
- BEM · beta-D-mannopyranuronic acid · sugar · 5 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 788 | 0.73 | 0.78 | 70 | BEM, MAW |
| 2 | 258 | 0.49 | 0.74 | 29 | BEM |
| 3 | 81 | 0.38 | 0.77 | 16 | empty |
| 4 | 85 | 0.36 | 0.75 | 15 | empty |
| 5 | 89 | 0.36 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 347 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4F13 · Alginate lyase A1-III Y246F complexed with tetrasaccharide · 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 Q9KWU1
- Elsewhere: RCSB PDB 4F13 · PDBe 4F13 · UniProt Q9KWU1
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