Research workbench
Structure of the staphylococcus aureus agra lyttr domain bound to DNA reveals a beta fold with a novel mode of binding
Analyse Structure of the staphylococcus aureus agra lyttr domain bound to DNA reveals a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BS1
- Type
- protein + DNA
- Length
- 135 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Accessory gene regulator protein a; DNA (5'- D(*DTP*DTP*DTP*DAP*DAP*DCP*DAP*DGP*DTP*DTP*DA…
- UniProt
- P0A0I7
- Ligands
- MG
- Pockets
- 5 · best druggability 0.40
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Accessory gene regulator protein a | protein | 103 | 16% helix, 49% strand | P0A0I7 |
| B | DNA (5'- D(*DTP*DTP*DTP*DAP*DAP*DCP*DAP*DGP*DTP*DTP*DAP*DAP*DGP*(BRU )P*DAP*DT)-3') | dna | 16 | — | — |
| C | DNA (5'-D(*DAP*DAP*(BRU) P*DAP*DCP*DTP*DTP*DAP*DAP*DCP*DTP*DGP*DTP*DTP*DAP*DA)-3') | dna | 16 | — | — |
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
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 110 | 0.40 | 0.76 | 23 | empty |
| 2 | 80 | 0.32 | 0.74 | 12 | empty |
| 3 | 51 | 0.28 | 0.75 | 17 | empty |
| 4 | 51 | 0.28 | 0.75 | 10 | empty |
| 5 | 50 | 0.24 | 0.72 | 10 | empty |
Interfaces
3 interfaces between chains.
- B–C · 665 Ų buried · 56 hydrogen bonds · nucleic-nucleic
- A–C · 513 Ų buried · 9 hydrogen bonds · protein-nucleic
- A–B · 350 Ų buried · 9 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 3BS1 · Structure of the Staphylococcus aureus AgrA LytTR Domain Bound to DNA Reveals a Beta Fold… · the same entry in another collection · chain A against A, TM-score 1.00
- P0A0I7 · AlphaFold monomer V2.0 prediction for accessory gene regulator protein a (P0A0I7) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P0A0I7
- Elsewhere: RCSB PDB 3BS1 · PDBe 3BS1 · UniProt P0A0I7
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