MolNFT v2 · #216914 · protein + DNA
Structure of Escherichia coli HrpA in complex with ADP and dinucleotide dCdC
8PO7 · ATP-dependent RNA helicase HrpA: “Structure of Escherichia coli HrpA in complex with ADP and dinucleotide dCdC”. X-ray diffraction at 2.26, 3 ligands (ADP, MG, PO4), 14 pockets (best druggability 0.84). MolNFT v2 #216914 on…
- 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
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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