Research workbench
Complex structure of LOR107 mutant (R320) with tetrasaccharide substrate
Analyse Complex structure of LOR107 mutant (R320) with tetrasaccharide substrate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BYT
- Type
- protein
- Length
- 962 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Short ulvan lyase
- UniProt
- A0A109PTH9
- Ligands
- 83Y, GCD, BDP, CA, SO4
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Short ulvan lyase | protein | 480 | 6% helix, 44% strand | A0A109PTH9 |
| B | Short ulvan lyase | protein | 482 | 6% helix, 44% strand | A0A109PTH9 |
Ligands and binding sites
- 83Y · 3-O-sulfo-alpha-L-rhamnopyranose · ligand · 4 copies · chains A, B
- GCD · 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid · ligand · 2 copies · chains A, B
- BDP · beta-D-glucopyranuronic acid · sugar · 2 copies · chains A, B
- CA · Calcium ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 7 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
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 967 | 0.78 | 0.80 | 83 | 83Y, BDP |
| 2 | 1027 | 0.78 | 0.80 | 96 | BDP, 83Y |
| 3 | 83 | 0.38 | 0.77 | 19 | empty |
| 4 | 81 | 0.37 | 0.77 | 23 | empty |
| 5 | 108 | 0.35 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 315 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6BYT · Complex structure of LOR107 mutant (R320) with tetrasaccharide substrate · 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 A0A109PTH9
- Elsewhere: RCSB PDB 6BYT · PDBe 6BYT · UniProt A0A109PTH9
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