MolNFT v1 · #12141 · protein
Crystal structure analysis of crosslinked-WGA3/GLCNACBETA1,6GALBETA1, 4GLC
1K7V · Agglutinin isolectin 3: “Crystal structure analysis of crosslinked-WGA3/GLCNACBETA1,6GALBETA1, 4GLC”. X-ray diffraction, 3 ligands (BGC, GAL, NAG), 3 pockets (best druggability 0.67). MolNFT v1 #12141 on GenesisL1: 3D structure…
- PDB
- 1K7V
- Type
- protein
- Length
- 342 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Agglutinin isolectin 3
- UniProt
- P10969
- Ligands
- BGC, GAL, NAG
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 21% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Agglutinin isolectin 3 | protein | 171 | 21% helix, 18% strand | P10969 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 2 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 104 | 0.67 | 0.91 | 30 | empty |
| 2 | 91 | 0.61 | 0.89 | 20 | empty |
| 3 | 56 | 0.60 | 0.92 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 2412 Ų buried · 42 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 disulfide, 2 modified (disulfide, cyclization).
Compared structures
- 1K7V · Crystal Structure Analysis of crosslinked-WGA3/GlcNAcbeta1,6Galbeta1,4Glc · the same entry in another collection · chain A against A, TM-score 1.00
- P10969 · AlphaFold monomer V2.0 prediction for agglutinin isolectin 3 (P10969) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P10969
- Elsewhere: RCSB PDB 1K7V · PDBe 1K7V · UniProt P10969
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