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
- 4R6Q
- Type
- protein
- Length
- 593 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
- NBZ, GLA
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 0% helix, 61% 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 | 16 | 0% helix, 44% strand | P18673 |
| D | Agglutinin beta-3 chain | protein | 15 | 0% helix, 47% strand | P18673 |
| F, H | Agglutinin beta-3 chain | protein | 15 | 0% helix, 47% strand | P18673 |
Ligands and binding sites
- NBZ · Nitrobenzene · ligand · 4 copies · chains A, C, E, G
- GLA · alpha-D-galactopyranose · sugar · 4 copies · chains A, C, E, G
- EDO · 1,2-ethanediol · additive · 5 copies · chains B, E, C, F, D, G, H
- IPA · Isopropyl alcohol · additive · 3 copies · chains C, G, A, E, H
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 | 531 | 0.82 | 0.89 | 73 | IPA |
| 2 | 69 | 0.33 | 0.76 | 15 | EDO |
| 3 | 68 | 0.29 | 0.73 | 18 | empty |
| 4 | 57 | 0.29 | 0.75 | 14 | EDO |
| 5 | 58 | 0.28 | 0.74 | 20 | empty |
Interfaces
22 interfaces between chains.
- E–F · 564 Ų buried · 7 hydrogen bonds · protein-protein
- G–H · 540 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 534 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 526 Ų buried · 8 hydrogen bonds · protein-protein
- E–H · 427 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4R6Q · Jacalin-carbohydrate interactions. Distortion of the ligand as a determinant of affinity. · 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 4R6Q · PDBe 4R6Q · UniProt P18670 · UniProt P18673
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