Research workbench
Three dimensional structure of the giant reed (arundodonax) lectin (adl) complex with N-acetyl lactosamine
Analyse Three dimensional structure of the giant reed (arundodonax) lectin (adl)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6STO
- Type
- protein
- Length
- 330 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arundo donax lectin (adl)
- Ligands
- NAG, GAL
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Arundo donax lectin (adl) | protein | 165 | 21% helix, 21% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · chains A, B
- GOL · Glycerol · additive · chains A
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 | 134 | 0.63 | 0.86 | 36 | NAG |
| 2 | 132 | 0.63 | 0.86 | 33 | NAG |
| 3 | 78 | 0.37 | 0.77 | 21 | empty |
| 4 | 61 | 0.36 | 0.79 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 2240 Ų buried · 45 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 34 disulfide (disulfide).
Compared structures
- 6STO · Three dimensional structure of the giant reed (Arundodonax) lectin (ADL) complex with… · 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 6STO · PDBe 6STO
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