Research workbench
ARBITRIUM PEPTIDE RECEPTOR FROM SPBETA PHAGE in complex with 43 mer DNA
Analyse ARBITRIUM PEPTIDE RECEPTOR FROM SPBETA PHAGE in complex with 43 mer DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HP7
- Type
- protein + DNA
- Length
- 858 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.2
- Source
- Bacillus subtilis (strain 168); SYNTHETIC CONSTRUCT
- Molecule
- SPBc2 prophage-derived uncharacterized protein YopK; DNA (43-mer)
- UniProt
- O31927
- Ligands
- PO4
- Pockets
- 15 · best druggability 0.70
Structure
x-ray diffraction · resolution 2.2 · 3 distinct chains · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | SPBc2 prophage-derived uncharacterized protein YopK | protein | 386 | 72% helix, 0% strand | O31927 |
| C | DNA (43-mer) | dna | 43 | — | — |
| D | DNA (43-mer) | dna | 43 | — | — |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 6 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 617 | 0.70 | 0.78 | 59 | empty |
| 2 | 686 | 0.69 | 0.77 | 46 | empty |
| 3 | 573 | 0.65 | 0.76 | 50 | PO4 |
| 4 | 490 | 0.63 | 0.76 | 39 | empty |
| 5 | 429 | 0.62 | 0.76 | 36 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1898 Ų buried · 171 hydrogen bonds · nucleic-nucleic
- A–B · 1430 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 618 Ų buried · 12 hydrogen bonds · protein-nucleic
- B–D · 612 Ų buried · 11 hydrogen bonds · protein-nucleic
- B–C · 476 Ų buried · 14 hydrogen bonds · protein-nucleic
Compared structures
- 6HP7 · Arbitrium peptide receptor from spbeta phage in complex with 43 mer DNA · the same entry in another collection · chain A against A, TM-score 1.00
- O31927 · AlphaFold monomer V2.0 prediction for spbeta prophage-derived uncharacterized protein… · 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 O31927
- Elsewhere: RCSB PDB 6HP7 · PDBe 6HP7 · UniProt O31927
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