Research workbench
Structure of alginate lyase ALYC3 in complex with DIMANNURONATE(2M)
Analyse Structure of alginate lyase ALYC3 in complex with DIMANNURONATE(2M) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7C8F
- Type
- protein
- Length
- 532 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- H127A/Y244A mutant of alginate lyase ALYC3 in complex with dimannuronate
- Ligands
- BEM
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 9% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | H127A/Y244A mutant of alginate lyase ALYC3 in complex with dimannuronate | protein | 266 | 9% helix, 46% strand | — |
Ligands and binding sites
- BEM · beta-D-mannopyranuronic acid · sugar · 4 copies · chains A, B
- MLI · Malonate ion · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 410 | 0.65 | 0.79 | 42 | empty |
| 2 | 224 | 0.46 | 0.74 | 32 | BEM |
| 3 | 156 | 0.41 | 0.74 | 27 | BEM |
| 4 | 70 | 0.30 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 460 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7C8F · Structure of alginate lyase AlyC3 in complex with dimannuronate(2M) · 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
- Elsewhere: RCSB PDB 7C8F · PDBe 7C8F
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