Research workbench
Wisteria floribunda lectin in complex with galnac
Analyse Wisteria floribunda lectin in complex with galnac in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KXB
- Type
- protein
- Length
- 952 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Wisteria floribunda agglutinin
- Ligands
- NAG, NGA, BMA, FUC, XYP, MAN, CA, MN
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 7% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Wisteria floribunda agglutinin | protein | 238 | 7% helix, 47% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B, C
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · 4 copies · chains A, B, C, D
- BMA · beta-D-mannopyranose · sugar · 3 copies
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains C
- XYP · beta-D-xylopyranose · sugar
- MAN · alpha-D-mannopyranose · sugar
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
- MN · Manganese (II) 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
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 646 | 0.71 | 0.79 | 64 | empty |
| 2 | 608 | 0.70 | 0.79 | 59 | empty |
| 3 | 66 | 0.44 | 0.82 | 19 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1155 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1155 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 614 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 605 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 13 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 glycan (N-glycosylation).
Compared structures
- 5KXB · Wisteria floribunda lectin in complex with GalNAc · 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 5KXB · PDBe 5KXB
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