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Crystal structure of the catalytic module of a family 98 glycoside hydrolase from streptococcus pneumoniae SP3-BS71 (SP3GH98) in complex with the a-lewisy pentasaccharide 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
- 2WMK
- Type
- protein
- Length
- 1,145 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fucolectin-related protein
- UniProt
- A5LBQ0
- Ligands
- FUC, NAG, GAL, A2G
- Pockets
- 9 · best druggability 0.63
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 | 573 | 32% helix, 26% strand | A5LBQ0 |
Ligands and binding sites
- FUC · alpha-L-fucopyranose · sugar · 4 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- GAL · beta-D-galactopyranose · sugar · 2 copies · chains A, B
- A2G · 2-acetamido-2-deoxy-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
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 326 | 0.63 | 0.79 | 37 | NAG, GAL, FUC, A2G |
| 2 | 323 | 0.63 | 0.79 | 43 | NAG, GAL, FUC, A2G |
| 3 | 64 | 0.50 | 0.86 | 18 | empty |
| 4 | 128 | 0.48 | 0.79 | 21 | empty |
| 5 | 120 | 0.45 | 0.78 | 23 | empty |
Compared structures
- 2WMK · 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 2WMK · PDBe 2WMK · UniProt A5LBQ0
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