Research workbench
Crystal structure of jacalin- galnac-BETA(1-3)-gal-alpha-O-me complex
Analyse Crystal structure of jacalin- galnac-BETA(1-3)-gal-alpha-O-me complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1UH1
- Type
- protein
- Length
- 592 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, MGC, NGA
- Pockets
- 4 · best druggability 0.40
Structure
x-ray diffraction · 2 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, 67% strand | P18670 |
| B, D, F, H | Agglutinin beta-3 chain | protein | 15 | 0% helix, 47% strand | P18673 |
Ligands and binding sites
- AMG · methyl alpha-D-galactopyranoside · ligand · 3 copies · chains C, E, G
- MGC · methyl 2-acetamido-2-deoxy-alpha-D-galactopyranoside · ligand · chains A
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · 3 copies · chains C, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 150 | 0.40 | 0.73 | 26 | empty |
| 2 | 146 | 0.40 | 0.74 | 27 | empty |
| 3 | 126 | 0.39 | 0.74 | 25 | empty |
| 4 | 116 | 0.35 | 0.73 | 22 | empty |
Interfaces
12 interfaces between chains.
- C–D · 534 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 534 Ų buried · 7 hydrogen bonds · protein-protein
- G–H · 532 Ų buried · 7 hydrogen bonds · protein-protein
- E–F · 530 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 452 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 1UH1 · Crystal structure of jacalin- GalNAc-beta(1-3)-Gal-alpha-O-Me complex · 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 0.32
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 1UH1 · PDBe 1UH1 · UniProt P18670 · UniProt P18673
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