Research workbench
Mechanistic basis of plasmid-specific DNA binding of the F plasmid regulatory protein, tram
Analyse Mechanistic basis of plasmid-specific DNA binding of the F plasmid regulatory… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QPQ
- Type
- protein + DNA
- Length
- 465 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Relaxosome protein tram; Sbma DNA1; Sbma DNA2
- UniProt
- P10026
- Pockets
- 8 · best druggability 0.61
Structure
x-ray diffraction · 5 distinct chains · 67% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, G | Relaxosome protein tram | protein | 50 | 66% helix, 10% strand | P10026 |
| B, C, D, F | Relaxosome protein tram | protein | 52 | 67% helix, 10% strand | P10026 |
| H | Relaxosome protein tram | protein | 51 | 67% helix, 10% strand | P10026 |
| P | Sbma DNA1 | dna | 28 | — | — |
| Q | Sbma DNA2 | dna | 28 | — | — |
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 355 | 0.61 | 0.78 | 32 | empty |
| 2 | 318 | 0.54 | 0.75 | 28 | empty |
| 3 | 282 | 0.52 | 0.75 | 27 | empty |
| 4 | 77 | 0.39 | 0.78 | 12 | empty |
| 5 | 65 | 0.39 | 0.79 | 12 | empty |
Interfaces
21 interfaces between chains.
- B–C · 1477 Ų buried · 17 hydrogen bonds · protein-protein
- F–G · 1473 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 1469 Ų buried · 16 hydrogen bonds · protein-protein
- E–H · 1468 Ų buried · 16 hydrogen bonds · protein-protein
- P–Q · 1280 Ų buried · 125 hydrogen bonds · nucleic-nucleic
Compared structures
- 4QPQ · Mechanistic basis of plasmid-specific DNA binding of the F plasmid regulatory protein… · the same entry in another collection · chain Q against Q, TM-score 1.00
- P10026 · AlphaFold monomer V2.0 prediction for relaxosome protein tram (P10026) · a predicted model of the same protein · chain H against A, TM-score 0.93
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 P10026
- Elsewhere: RCSB PDB 4QPQ · PDBe 4QPQ · UniProt P10026
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