MolNFT v1 · #88814 · protein
Crystal structure of a family 98 glycoside hydrolase catalytic module (SP3GH98) in complex with the type 1 blood group a-tetrasaccharide (E558A L19 mutant)
4D6I: “Crystal structure of a family 98 glycoside hydrolase catalytic module (SP3GH98) in complex with the type 1…”. X-ray diffraction, 4 ligands (NAG, GAL, FUC), 5 pockets (best druggability 0.62). MolNFT v1 #88814 on GenesisL1: 3D…
- PDB
- 4D6I
- 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
- Pockets
- 5 · 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
- 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 310 | 0.62 | 0.79 | 35 | NAG, GAL, FUC, A2G |
| 2 | 110 | 0.47 | 0.79 | 26 | empty |
| 3 | 52 | 0.37 | 0.81 | 16 | empty |
| 4 | 68 | 0.37 | 0.78 | 19 | empty |
| 5 | 66 | 0.30 | 0.74 | 16 | empty |
Compared structures
- 4D6I · 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 4D6I · PDBe 4D6I · UniProt A5LBQ0
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