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Crystal structure of the catalytic module of a family 98 glycoside hydrolase from streptococcus pneumoniae TIGR4 (SP4GH98) in complex with the 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
- 2WMG
- Type
- protein
- Length
- 553 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fucolectin-related protein
- UniProt
- Q97N96
- Ligands
- FUC, NAG, GAL
- Pockets
- 5 · best druggability 0.60
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fucolectin-related protein | protein | 553 | 32% helix, 25% strand | Q97N96 |
Ligands and binding sites
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- GAL · beta-D-galactopyranose · sugar · 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 | 270 | 0.60 | 0.78 | 26 | NAG, GAL, FUC |
| 2 | 121 | 0.46 | 0.78 | 30 | empty |
| 3 | 59 | 0.34 | 0.77 | 13 | empty |
| 4 | 59 | 0.34 | 0.77 | 17 | empty |
| 5 | 61 | 0.30 | 0.75 | 15 | empty |
Compared structures
- 2WMG · 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 Q97N96
- Elsewhere: RCSB PDB 2WMG · PDBe 2WMG · UniProt Q97N96
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