Research workbench
Crystal structure of icar from staphylococcus aureus, a member of the tetracycline repressor protein family
Analyse Crystal structure of icar from staphylococcus aureus, a member of the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GEU
- Type
- protein
- Length
- 756 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Intercellular adhesion protein R
- UniProt
- Q5HCN2
- Ligands
- NA, CL
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 78% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Intercellular adhesion protein R | protein | 189 | 78% helix, 1% strand | Q5HCN2 |
Ligands and binding sites
- NA · Sodium ion · metal · chains C
- CL · Chloride ion · ion · 5 copies · chains A, B, C
- FMT · Formic acid · additive · 10 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 863 | 0.69 | 0.75 | 75 | empty |
| 2 | 207 | 0.59 | 0.81 | 25 | empty |
| 3 | 244 | 0.59 | 0.79 | 25 | empty |
| 4 | 117 | 0.52 | 0.82 | 20 | empty |
| 5 | 76 | 0.42 | 0.80 | 20 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1877 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1826 Ų buried · 18 hydrogen bonds · protein-protein
- A–D · 139 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 45 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 33 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 3GEU · Crystal Structure of IcaR from Staphylococcus aureus, a member of the tetracycline… · the same entry in another collection · chain A against A, TM-score 1.00
- Q5HCN2 · AlphaFold monomer V2.0 prediction for biofilm operon icaadbc hth-type negative… · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q5HCN2
- Elsewhere: RCSB PDB 3GEU · PDBe 3GEU · UniProt Q5HCN2
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