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The X-ray crystal structure of tandem CBM51 modules of SP3GH98, the family 98 glycoside hydrolase from streptococcus pneumoniae SP3-BS71, in complex with the blood group B antigen
Analyse The X-ray crystal structure of tandem CBM51 modules of SP3GH98, the family 98… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YGM
- Type
- protein
- Length
- 703 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Blood group a-and B-cleaving endo-beta-galactosidase
- UniProt
- C1CB04
- Ligands
- NAG, GAL, FUC, GLA, CA, NA
- Pockets
- 8 · best druggability 0.51
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Blood group a-and B-cleaving endo-beta-galactosidase | protein | 351 | 7% helix, 42% strand | C1CB04 |
| B | Blood group a-and B-cleaving endo-beta-galactosidase | protein | 352 | 9% helix, 43% strand | C1CB04 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- 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
- CA · Calcium ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 155 | 0.51 | 0.79 | 28 | empty |
| 2 | 201 | 0.46 | 0.74 | 29 | empty |
| 3 | 83 | 0.45 | 0.81 | 18 | empty |
| 4 | 58 | 0.41 | 0.81 | 18 | empty |
| 5 | 133 | 0.41 | 0.75 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 720 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2YGM · The X-ray crystal structure of tandem CBM51 modules of SP3GH98, the family 98 glycoside… · 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 C1CB04
- Elsewhere: RCSB PDB 2YGM · PDBe 2YGM · UniProt C1CB04
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