Research workbench
Crystal structure of the catalytic module of a family 98 glycoside hydrolase from streptococcus pneumoniae SP3-BS71 (SP3GH98) in complex with the B-trisaccharide blood group antigen.
Analyse Crystal structure of the catalytic module of a family 98 glycoside hydrolase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WMJ
- Type
- protein
- Length
- 1,143 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fucolectin-related protein
- UniProt
- A5LBQ0
- Ligands
- GAL, FUC, GLA
- Pockets
- 10 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fucolectin-related protein | protein | 572 | 33% helix, 25% strand | A5LBQ0 |
| B | Fucolectin-related protein | protein | 571 | 33% helix, 26% strand | A5LBQ0 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B
- GLA · alpha-D-galactopyranose · sugar · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 311 | 0.64 | 0.80 | 42 | GAL, FUC, GLA |
| 2 | 309 | 0.62 | 0.79 | 45 | GAL, FUC, GLA |
| 3 | 64 | 0.53 | 0.87 | 22 | empty |
| 4 | 133 | 0.47 | 0.78 | 22 | empty |
| 5 | 116 | 0.45 | 0.78 | 23 | empty |
Compared structures
- 2WMJ · Crystal structure of the catalytic module of a family 98 glycoside hydrolase from… · 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 2WMJ · PDBe 2WMJ · UniProt A5LBQ0
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