MolNFT v1 · #88813 · protein
Crystal structure of a family 98 glycoside hydrolase catalytic module (SP3GH98) in complex with the type 1 blood group a-tetrasaccharide (E558A X02 mutant)
4D6H: “Crystal structure of a family 98 glycoside hydrolase catalytic module (SP3GH98) in complex with the type 1…”. X-ray diffraction, 5 ligands (NAG, GAL, FUC), 6 pockets (best druggability 0.62). MolNFT v1 #88813 on GenesisL1: 3D…
- PDB
- 4D6H
- Type
- protein
- Length
- 587 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
- NAG, GAL, FUC, A2G, SO4
- Pockets
- 6 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycoside hydrolase (EC 3.2.1.102) | protein | 587 | 34% helix, 25% strand | A5LBQ0 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- 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 · 4 copies · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 331 | 0.62 | 0.78 | 36 | NAG, GAL, FUC, A2G |
| 2 | 94 | 0.50 | 0.83 | 19 | empty |
| 3 | 118 | 0.47 | 0.79 | 25 | empty |
| 4 | 61 | 0.34 | 0.77 | 17 | empty |
| 5 | 72 | 0.30 | 0.74 | 16 | empty |
Compared structures
- 4D6H · 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 4D6H · PDBe 4D6H · UniProt A5LBQ0
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