MolNFT v1 · #140971 · protein
Crystal structure of beta-1,2-glucooligosaccharide binding protein in complex with sophorotriose
5YSD · LIN1841 protein: “Crystal structure of beta-1,2-glucooligosaccharide binding protein in complex with sophorotriose”. X-ray diffraction, 3 ligands (BGC, GLC, MG), 5 pockets (best druggability 0.74). MolNFT v1 #140971 on GenesisL1: 3D…
- PDB
- 5YSD
- Type
- protein
- Length
- 776 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- LIN1841 protein
- UniProt
- Q92AS8
- Ligands
- BGC, GLC, MG
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | LIN1841 protein | protein | 387 | 50% helix, 16% strand | Q92AS8 |
| B | LIN1841 protein | protein | 389 | 49% helix, 16% strand | Q92AS8 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 4 copies · chains A, B
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A, B
- MG · Magnesium ion · metal · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 510 | 0.74 | 0.82 | 55 | GLC, BGC, MPD |
| 2 | 566 | 0.73 | 0.81 | 63 | GLC, BGC, MPD |
| 3 | 444 | 0.68 | 0.80 | 53 | empty |
| 4 | 66 | 0.30 | 0.74 | 19 | empty |
| 5 | 73 | 0.29 | 0.72 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 476 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 5YSD · Crystal structure of beta-1,2-glucooligosaccharide binding protein in complex with… · 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 Q92AS8
- Elsewhere: RCSB PDB 5YSD · PDBe 5YSD · UniProt Q92AS8
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