Research workbench
Crystal structure of jacalin
Analyse Crystal structure of jacalin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1KU8
- Type
- protein
- Length
- 596 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Jacalin alpha chain; Jacalin beta chain
- UniProt
- P18670, P18671
- Pockets
- 5 · 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 | Jacalin alpha chain | protein | 133 | 0% helix, 67% strand | P18670 |
| B | Jacalin beta chain | protein | 18 | 0% helix, 39% strand | P18671 |
| D | Jacalin beta chain | protein | 16 | 0% helix, 38% strand | P18671 |
| F | Jacalin beta chain | protein | 15 | 0% helix, 47% strand | P18671 |
| H | Jacalin beta chain | protein | 15 | 0% helix, 47% strand | P18671 |
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 570 | 0.82 | 0.88 | 76 | empty |
| 2 | 158 | 0.50 | 0.78 | 24 | empty |
| 3 | 83 | 0.32 | 0.74 | 25 | empty |
| 4 | 69 | 0.30 | 0.74 | 16 | empty |
| 5 | 53 | 0.27 | 0.74 | 20 | empty |
Interfaces
22 interfaces between chains.
- C–D · 545 Ų buried · 7 hydrogen bonds · protein-protein
- G–H · 543 Ų buried · 8 hydrogen bonds · protein-protein
- E–F · 539 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 531 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 434 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 1KU8 · Crystal structure of Jacalin · 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
- P18671 · AlphaFold monomer V2.0 prediction for agglutinin beta-1 chain (P18671) · a predicted model of the same protein · chain H against A, TM-score 0.31
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 P18671
- Elsewhere: RCSB PDB 1KU8 · PDBe 1KU8 · UniProt P18670 · UniProt P18671
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