Research workbench
RfaH from Escherichia coli in complex with ops DNA
Analyse RfaH from Escherichia coli in complex with ops DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OND
- Type
- protein + DNA
- Length
- 286 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.1
- Source
- Escherichia coli; SYNTHETIC CONSTRUCT
- Molecule
- Transcription antitermination protein RfaH; DNA (5'-D(*GP*CP*GP*GP*TP*AP*GP*TP*C)-3')
- UniProt
- P0AFW0
- Pockets
- 2 · best druggability 0.60
Structure
x-ray diffraction · resolution 2.1 · 3 distinct chains · 38% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcription antitermination protein RfaH | protein | 135 | 39% helix, 30% strand | P0AFW0 |
| B | Transcription antitermination protein RfaH | protein | 133 | 38% helix, 32% strand | P0AFW0 |
| C, D | DNA (5'-D(*GP*CP*GP*GP*TP*AP*GP*TP*C)-3') | dna | 9 | — | — |
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 303 | 0.60 | 0.77 | 20 | empty |
| 2 | 179 | 0.43 | 0.74 | 44 | empty |
Interfaces
3 interfaces between chains.
- A–B · 959 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 439 Ų buried · 14 hydrogen bonds · protein-nucleic
- B–D · 433 Ų buried · 14 hydrogen bonds · protein-nucleic
Compared structures
- 5OND · Rfah from escherichia COLI in complex with ops DNA · the same entry in another collection · chain A against A, TM-score 1.00
- P0AFW0 · AlphaFold monomer V2.0 prediction for transcription antitermination protein rfah (P0AFW0) · a predicted model of the same protein · chain B against A, TM-score 0.91
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 P0AFW0
- Elsewhere: RCSB PDB 5OND · PDBe 5OND · UniProt P0AFW0
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