MolNFT v1 · #19560 · protein
Lectin II from ulex europaeus
1QNW · Chitin binding lectin, uea-II: “Lectin II from ulex europaeus”. X-ray diffraction, 3 ligands (NAG, MN, CA), 5 pockets (best druggability 0.82). MolNFT v1 #19560 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1QNW
- Type
- protein
- Length
- 942 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chitin binding lectin, uea-II
- Ligands
- NAG, MN, CA
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chitin binding lectin, uea-II | protein | 234 | 6% helix, 44% strand | — |
| B, C, D | Chitin binding lectin, uea-II | protein | 236 | 6% helix, 43% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1090 | 0.82 | 0.84 | 104 | empty |
| 2 | 156 | 0.63 | 0.85 | 23 | empty |
| 3 | 148 | 0.63 | 0.85 | 23 | empty |
| 4 | 122 | 0.61 | 0.86 | 21 | empty |
| 5 | 166 | 0.61 | 0.83 | 24 | empty |
Interfaces
6 interfaces between chains.
- A–B · 852 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 842 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 750 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 748 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 80 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 glycan, 2 disulfide (O-glycosylation, disulfide).
Compared structures
- 1QNW · lectin II from Ulex europaeus · the same entry in another collection · chain C against C, 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 1QNW · PDBe 1QNW
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