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Structure of tetrameric jacalin complexed with a trisaccharide, gal alpha-(1,3) gal beta-(1,4) gal
Analyse Structure of tetrameric jacalin complexed with a trisaccharide, gal alpha-(1,3)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JM1
- Type
- protein
- Length
- 591 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Agglutinin alpha chain; Agglutinin beta-3 chain
- UniProt
- P18670, P18673
- Ligands
- AMG, GAL, GLA
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 0% helix, 63% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Agglutinin alpha chain | protein | 133 | 0% helix, 67% strand | P18670 |
| B, F, H | Agglutinin beta-3 chain | protein | 15 | 0% helix, 47% strand | P18673 |
| D | Agglutinin beta-3 chain | protein | 14 | 0% helix, 43% strand | P18673 |
Ligands and binding sites
- AMG · methyl alpha-D-galactopyranoside · ligand · chains G
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains E
- GLA · alpha-D-galactopyranose · sugar · chains E
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, F, C, D, G, E
- PEG · Di(hydroxyethyl)ether · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 510 | 0.82 | 0.89 | 74 | EDO |
| 2 | 56 | 0.34 | 0.78 | 13 | EDO |
| 3 | 89 | 0.33 | 0.74 | 24 | empty |
| 4 | 94 | 0.33 | 0.73 | 18 | empty |
| 5 | 77 | 0.31 | 0.74 | 21 | empty |
Interfaces
21 interfaces between chains.
- E–F · 563 Ų buried · 8 hydrogen bonds · protein-protein
- G–H · 547 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 542 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 498 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 425 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5JM1 · Structure of tetrameric jacalin complexed with a trisaccharide, Gal alpha-(1,3) Gal… · the same entry in another collection · chain H against H, TM-score 1.00
- P18670 · AlphaFold monomer V2.0 prediction for agglutinin alpha chain (P18670) · a predicted model of the same protein · chain A against A, TM-score 1.00
- P18673 · AlphaFold monomer V2.0 prediction for agglutinin beta-3 chain (P18673) · a predicted model of the same protein · chain B against A, TM-score 0.36
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 P18670
- Every structure of UniProt P18673
- Elsewhere: RCSB PDB 5JM1 · PDBe 5JM1 · UniProt P18670 · UniProt P18673
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