Research workbench
Jacalin-carbohydrate interactions. distortion of the ligand as a determinant of affinity.
Analyse Jacalin-carbohydrate interactions. distortion of the ligand as a determinant of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4R6R
- 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
- 147
- Pockets
- 6 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 0% helix, 59% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Agglutinin alpha chain | protein | 133 | 0% helix, 67% strand | P18670 |
| B | Agglutinin beta-3 chain | protein | 17 | 0% helix, 41% strand | P18673 |
| D | Agglutinin beta-3 chain | protein | 14 | 0% helix, 43% strand | P18673 |
| F | Agglutinin beta-3 chain | protein | 16 | 0% helix, 44% strand | P18673 |
| H | Agglutinin beta-3 chain | protein | 15 | 0% helix, 47% strand | P18673 |
Ligands and binding sites
- 147 · 4-nitrophenyl beta-D-galactopyranoside · ligand · 3 copies · chains A, E, G
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, E, C, D, G
- IPA · Isopropyl alcohol · additive · chains A
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 | 555 | 0.82 | 0.88 | 79 | empty |
| 2 | 110 | 0.41 | 0.76 | 22 | empty |
| 3 | 76 | 0.32 | 0.74 | 21 | empty |
| 4 | 69 | 0.30 | 0.74 | 19 | empty |
| 5 | 56 | 0.27 | 0.74 | 18 | empty |
Interfaces
21 interfaces between chains.
- E–F · 557 Ų buried · 7 hydrogen bonds · protein-protein
- G–H · 544 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 534 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 525 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 436 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4R6R · Jacalin-carbohydrate interactions. Distortion of the ligand as a determinant of affinity. · the same entry in another collection · chain F against F, 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 H against A, TM-score 0.35
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 4R6R · PDBe 4R6R · UniProt P18670 · UniProt P18673
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