Research workbench
Crystal structures reveal the multi-ligand binding mechanism of the staphylococcus aureus clfb
Analyse Crystal structures reveal the multi-ligand binding mechanism of the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4F20
- Type
- protein
- Length
- 342 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Clumping factor B; Peptide from dermokine
- UniProt
- Q6GDH2, Q6E0U4
- Ligands
- MG
- Pockets
- 2 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Clumping factor B | protein | 331 | 6% helix, 48% strand | Q6GDH2 |
| Q | Peptide from dermokine | protein | 11 | 0% helix, 55% strand | Q6E0U4 |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 282 | 0.61 | 0.79 | 36 | empty |
| 2 | 119 | 0.49 | 0.80 | 22 | empty |
Interfaces
1 interface between chains.
- A–Q · 753 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 4F20 · Crystal structures reveal the multi-ligand binding mechanism of the Staphylococcus aureus… · the same entry in another collection · chain A against A, TM-score 1.00
- Q6GDH2 · AlphaFold monomer V2.0 prediction for clumping factor B (Q6GDH2) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q6E0U4 · AlphaFold monomer V2.0 prediction for dermokine (Q6E0U4) · a predicted model of the same protein · chain Q against A, TM-score 0.39
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 Q6GDH2
- Every structure of UniProt Q6E0U4
- Elsewhere: RCSB PDB 4F20 · PDBe 4F20 · UniProt Q6GDH2 · UniProt Q6E0U4
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