Research workbench
Structure of Escherichia coli HrpA in complex with ADP and dinucleotide dCdC
Analyse Structure of Escherichia coli HrpA in complex with ADP and dinucleotide dCdC in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8PO7
- Type
- protein + DNA
- Length
- 1,175 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.26
- Source
- Escherichia coli K-12; SYNTHETIC CONSTRUCT
- Molecule
- ATP-dependent RNA helicase HrpA; DNA (5'-D(P*CP*C)-3')
- EC
- 3.6.4.13
- UniProt
- P43329
- Ligands
- ADP, MG, PO4
- Pockets
- 14 · best druggability 0.84
Structure
x-ray diffraction · resolution 2.26 · 3 distinct chains · 46% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ATP-dependent RNA helicase HrpA (EC 3.6.4.13) | protein | 594 | 47% helix, 14% strand | P43329 |
| B | ATP-dependent RNA helicase HrpA (EC 3.6.4.13) | protein | 579 | 45% helix, 15% strand | P43329 |
| C | DNA (5'-D(P*CP*C)-3') | dna | 2 | — | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1058 | 0.84 | 0.85 | 108 | ADP, MG |
| 2 | 542 | 0.78 | 0.85 | 69 | empty |
| 3 | 324 | 0.75 | 0.87 | 38 | ADP, MG |
| 4 | 510 | 0.74 | 0.83 | 59 | empty |
| 5 | 255 | 0.56 | 0.77 | 35 | empty |
Interfaces
2 interfaces between chains.
- A–B · 607 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 258 Ų buried · 5 hydrogen bonds · protein-nucleic
Compared structures
- P43329 · AlphaFold monomer V2.0 prediction for ATP-dependent RNA helicase hrpa (P43329) · a predicted model of the same protein · chain A against A, TM-score 0.81
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 P43329
- Elsewhere: RCSB PDB 8PO7 · PDBe 8PO7 · UniProt P43329
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