Research workbench
Structure of boletus edulis lectin in complex with N,N-diacetyl chitobiose
Analyse Structure of boletus edulis lectin in complex with N,N-diacetyl chitobiose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QDU
- Type
- protein
- Length
- 568 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Boletus edulis lectin
- Ligands
- ACE, NAG
- Pockets
- 1 · best druggability 0.87
Structure
x-ray diffraction · 1 distinct chain · 11% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Boletus edulis lectin | protein | 142 | 11% helix, 52% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 992 | 0.87 | 0.88 | 78 | empty |
Interfaces
6 interfaces between chains.
- B–C · 892 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 869 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 688 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 680 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 141 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 3QDU · Structure of Boletus edulis lectin in complex with N,N-diacetyl chitobiose · 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 3QDU · PDBe 3QDU
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