MolNFT v1 · #88810 · protein
Crystal structure of a family 98 glycoside hydrolase catalytic module (SP3GH98) in complex with the blood group a-trisaccharide (X01 mutant)
4D6E: “Crystal structure of a family 98 glycoside hydrolase catalytic module (SP3GH98) in complex with the blood…”. X-ray diffraction, 4 ligands (GAL, FUC, A2G), 5 pockets (best druggability 0.60). MolNFT v1 #88810 on GenesisL1: 3D…
- PDB
- 4D6E
- Type
- protein
- Length
- 578 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glycoside hydrolase
- EC
- 3.2.1.102
- UniProt
- A5LBQ0
- Ligands
- GAL, FUC, A2G, SO4
- Pockets
- 5 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycoside hydrolase (EC 3.2.1.102) | protein | 578 | 32% helix, 26% strand | A5LBQ0 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · chains A
- FUC · alpha-L-fucopyranose · sugar · chains A
- A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · chains A
- SO4 · Sulfate ion · ion · 3 copies · chains A
- EDO · 1,2-ethanediol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 285 | 0.60 | 0.79 | 36 | GAL, FUC, A2G |
| 2 | 109 | 0.46 | 0.79 | 22 | empty |
| 3 | 83 | 0.34 | 0.74 | 16 | empty |
| 4 | 57 | 0.31 | 0.76 | 16 | empty |
| 5 | 52 | 0.27 | 0.74 | 17 | empty |
Compared structures
- 4D6E · Crystal structure of a family 98 glycoside hydrolase catalytic module (Sp3GH98) in… · 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 A5LBQ0
- Elsewhere: RCSB PDB 4D6E · PDBe 4D6E · UniProt A5LBQ0
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