Research workbench
Structure of a streptococcus pneumoniae fucose binding module in complex with the blood group a-tetrasaccharide
Analyse Structure of a streptococcus pneumoniae fucose binding module in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2J1U
- Type
- protein
- Length
- 277 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fucolectin-related protein
- UniProt
- Q97N96
- Ligands
- BGC, GAL, FUC, A2G, CA
- Pockets
- 3 · best druggability 0.47
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fucolectin-related protein | protein | 141 | 8% helix, 45% strand | Q97N96 |
| B | Fucolectin-related protein | protein | 136 | 8% helix, 46% strand | Q97N96 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · chains A
- GAL · beta-D-galactopyranose · sugar
- FUC · alpha-L-fucopyranose · sugar · chains A
- A2G · 2-acetamido-2-deoxy-alpha-D-galactopyranose · sugar · chains A
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 100 | 0.47 | 0.80 | 25 | empty |
| 2 | 61 | 0.36 | 0.78 | 19 | empty |
| 3 | 61 | 0.29 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 526 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 2J1U · Structure of a Streptococcus pneumoniae fucose binding module in complex with the blood… · 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 2J1U · PDBe 2J1U · UniProt Q97N96
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