Research workbench
Crystal structure of frutalin from artocarpus incisa in complex with galactose
Analyse Crystal structure of frutalin from artocarpus incisa in complex with galactose in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5BN6
- Type
- protein
- Length
- 602 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Jacalin
- UniProt
- Q38720
- Ligands
- GAL
- Pockets
- 4 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 0% helix, 61% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Jacalin | protein | 17 | 0% helix, 41% strand | Q38720 |
| E, F, G, H | Jacalin | protein | 133 | 0% helix, 67% strand | Q38720 |
| B | Jacalin | protein | 19 | 0% helix, 37% strand | Q38720 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 4 copies · chains 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 435 | 0.84 | 0.92 | 57 | empty |
| 2 | 66 | 0.28 | 0.73 | 19 | empty |
| 3 | 63 | 0.28 | 0.74 | 22 | empty |
| 4 | 54 | 0.28 | 0.75 | 13 | empty |
Interfaces
22 interfaces between chains.
- D–H · 563 Ų buried · 7 hydrogen bonds · protein-protein
- C–G · 563 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 560 Ų buried · 8 hydrogen bonds · protein-protein
- B–F · 551 Ų buried · 7 hydrogen bonds · protein-protein
- B–G · 444 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5BN6 · Crystal Structure of Frutalin from Artocarpus incisa in complex with galactose · the same entry in another collection · chain A against A, TM-score 1.00
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 Q38720
- Elsewhere: RCSB PDB 5BN6 · PDBe 5BN6 · UniProt Q38720
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