Research workbench
Structure of tetrameric jacalin complexed with gal beta-(1,3) galnac- alpha-opnp
Analyse Structure of tetrameric jacalin complexed with gal beta-(1,3) galnac- alpha-opnp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5J50
- Type
- protein
- Length
- 594 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
- NPO, A2G, GAL
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 0% helix, 65% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Agglutinin alpha chain | protein | 133 | 0% helix, 69% strand | P18670 |
| B, D | Agglutinin beta-3 chain | protein | 16 | 0% helix, 44% strand | P18673 |
| F, H | Agglutinin beta-3 chain | protein | 15 | 0% helix, 47% strand | P18673 |
Ligands and binding sites
- NPO · P-nitrophenol · ligand · 4 copies · chains A, C, E, G
- A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · 4 copies · chains A, C, E, G
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains A, B, C, D, E, F, G, H
- EDO · 1,2-ethanediol · additive · 12 copies · chains A, C, E, B, F, G, D, H
- PEG · Di(hydroxyethyl)ether · additive · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 570 | 0.83 | 0.89 | 71 | empty |
| 2 | 87 | 0.32 | 0.73 | 26 | empty |
| 3 | 55 | 0.30 | 0.76 | 15 | EDO |
| 4 | 71 | 0.29 | 0.73 | 20 | EDO |
| 5 | 59 | 0.28 | 0.74 | 18 | EDO |
Interfaces
21 interfaces between chains.
- A–B · 541 Ų buried · 8 hydrogen bonds · protein-protein
- G–H · 540 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 524 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 518 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 431 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 5J50 · Structure of tetrameric jacalin complexed with Gal beta-(1,3) GalNAc-alpha-OPNP · 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 F against A, TM-score 0.33
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 5J50 · PDBe 5J50 · UniProt P18670 · UniProt P18673
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