MolNFT v1 · #154491 · protein
Structure of alginate lyase ALY36B mutant K143A/Y185A in complex with alginate tetrasaccharide
6KCV: “Structure of alginate lyase ALY36B mutant K143A/Y185A in complex with alginate tetrasaccharide”. X-ray diffraction, 2 ligands (BEM, CA), 4 pockets (best druggability 0.70). MolNFT v1 #154491 on GenesisL1: 3D structure, binding sites…
- PDB
- 6KCV
- Type
- protein
- Length
- 732 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alginate lyase
- UniProt
- A0A249T061
- Ligands
- BEM, CA
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 1 distinct chain · 10% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A, C | Alginate lyase | protein | 244 | 10% helix, 47% strand | A0A249T061 |
Ligands and binding sites
- BEM · beta-D-mannopyranuronic acid · sugar · 12 copies · chains B, A, C
- CA · Calcium ion · metal · 3 copies · chains B, A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 782 | 0.70 | 0.77 | 91 | BEM |
| 2 | 233 | 0.51 | 0.75 | 39 | BEM |
| 3 | 147 | 0.45 | 0.76 | 23 | BEM |
| 4 | 101 | 0.43 | 0.78 | 19 | empty |
Interfaces
2 interfaces between chains.
- B–C · 433 Ų buried · 5 hydrogen bonds · protein-protein
- B–A · 367 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6KCV · Structure of alginate lyase Aly36B mutant K143A/Y185A in complex with alginate… · the same entry in another collection · chain B against B, 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 A0A249T061
- Elsewhere: RCSB PDB 6KCV · PDBe 6KCV · UniProt A0A249T061
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