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Crystal structure of a family 98 glycoside hydrolase catalytic module (SP3GH98) in complex with the type 2 blood group a-tetrasaccharide (E558A L19 mutant)
Analyse Crystal structure of a family 98 glycoside hydrolase catalytic module (SP3GH98)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4D72
- Type
- protein
- Length
- 586 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
- Pockets
- 5 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glycoside hydrolase (EC 3.2.1.102) | protein | 586 | 33% 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
- 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
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 | 305 | 0.59 | 0.77 | 34 | NAG, GAL, FUC, A2G |
| 2 | 87 | 0.53 | 0.85 | 20 | empty |
| 3 | 115 | 0.46 | 0.79 | 21 | empty |
| 4 | 59 | 0.36 | 0.79 | 13 | empty |
| 5 | 83 | 0.33 | 0.74 | 16 | empty |
Compared structures
- 4D72 · 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 4D72 · PDBe 4D72 · UniProt A5LBQ0
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