Research workbench
Crystal structure of SpaA-SLH in complex with beta-D-GlcNAc-(1->3)-4,6-Pyr-beta-D-ManNAcOMe
Analyse Crystal structure of SpaA-SLH 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
- 6CWL
- Type
- protein
- Length
- 310 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.15
- Source
- Paenibacillus alvei
- Molecule
- Surface (S-) layer glycoprotein
- UniProt
- C1JZ07
- Ligands
- FHY
- Pockets
- 3 · best druggability 0.67
Structure
x-ray diffraction · resolution 2.15 · 2 distinct chains · 43% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Surface (S-) layer glycoprotein | protein | 164 | 41% helix, 5% strand | C1JZ07 |
| B | Surface (S-) layer glycoprotein | protein | 146 | 45% helix, 5% strand | C1JZ07 |
Ligands and binding sites
- FHY · (2S,4aR,6R,7S,8R,8aS)-7-(acetylamino)-6-({2-(acetylamino)-3-O-[2-(acetylamino)-2-deoxy-beta-D-glucopyranosyl]-4,6-O-[(1S)-1-carboxylic acidethylidene]-2-deoxy-beta-D-mannopyranosyl}oxy)-8-{[2-(acetylamino)-2-deoxy-beta-D-glucopyranosyl]oxy}-2-methylhexahydro-2H-pyrano[3,2-d][1,3]dioxine-2-carboxylic acid · ligand · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 574 | 0.67 | 0.77 | 56 | empty |
| 2 | 117 | 0.39 | 0.75 | 24 | FHY |
| 3 | 63 | 0.37 | 0.78 | 12 | FHY |
Interfaces
1 interface between chains.
- A–B · 423 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6CWL · Crystal structure of spaa-slh in complex with beta-D-glcnac-(1->3)-4… · 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 C1JZ07
- Elsewhere: RCSB PDB 6CWL · PDBe 6CWL · UniProt C1JZ07
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