Research workbench
Lectin uea-II complexed with galactose
Analyse Lectin uea-II complexed with galactose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DZQ
- Type
- protein
- Length
- 942 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lectin II
- UniProt
- Q9FVF8
- Ligands
- NAG, GAL, MN, CA
- Pockets
- 5 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lectin II | protein | 234 | 7% helix, 45% strand | Q9FVF8 |
| B, C, D | Lectin II | protein | 236 | 7% helix, 44% strand | Q9FVF8 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B, C, D
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, C
- 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 | 1029 | 0.82 | 0.84 | 102 | empty |
| 2 | 60 | 0.62 | 0.92 | 21 | empty |
| 3 | 72 | 0.62 | 0.90 | 24 | empty |
| 4 | 67 | 0.60 | 0.90 | 21 | empty |
| 5 | 71 | 0.59 | 0.89 | 22 | empty |
Interfaces
6 interfaces between chains.
- A–B · 954 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 945 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 753 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 751 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 84 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 glycan, 2 disulfide (O-glycosylation, disulfide).
Compared structures
- 1DZQ · Lectin uea-II complexed with galactose · 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 Q9FVF8
- Elsewhere: RCSB PDB 1DZQ · PDBe 1DZQ · UniProt Q9FVF8
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