MolNFT v1 · #27641 · protein + RNA
Structural mechanism of inhibition of the rho transcription termination factor by the antibiotic 5A-(3-formylphenylsulfanyl)- dihydrobicyclomycin (fpdb)
1XPU · 5'-R(*CP*UP*CP*UP*CP*UP*CP*U)-3': “Structural mechanism of inhibition of the rho transcription termination factor by the antibiotic…”. X-ray diffraction, 3 ligands (AGS, FPD, MG), 20 pockets (best druggability 0.81). MolNFT v1…
- PDB
- 1XPU
- Type
- protein + RNA
- Length
- 2,459 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(*CP*UP*CP*UP*CP*UP*CP*U)-3'; Rho transcription termination factor
- UniProt
- P22869
- Ligands
- AGS, FPD, MG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G, M, H, J, K, L | 5'-R(*CP*UP*CP*UP*CP*UP*CP*U)-3' | rna | 2 | — | — |
| A, B, C, D, F | Rho transcription termination factor | protein | 408 | 41% helix, 21% strand | P22869 |
| E | Rho transcription termination factor | protein | 407 | 41% helix, 20% strand | P22869 |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 6 copies · chains A, B, C, D, E, F
- FPD · 5A-(3-formylphenylsulfanyl)-dihydrobicyclomycin · ligand · 5 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 983 | 0.81 | 0.83 | 74 | AGS, MG, FPD |
| 2 | 1001 | 0.80 | 0.82 | 78 | AGS, FPD |
| 3 | 937 | 0.80 | 0.82 | 73 | MG, AGS, FPD |
| 4 | 1103 | 0.79 | 0.81 | 70 | MG, AGS, FPD |
| 5 | 1136 | 0.79 | 0.81 | 95 | MG, AGS, FPD |
Interfaces
11 interfaces between chains.
- C–D · 1720 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 1682 Ų buried · 28 hydrogen bonds · protein-protein
- E–F · 1681 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1647 Ų buried · 22 hydrogen bonds · protein-protein
- D–E · 1632 Ų buried · 26 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 covalent (covalent ligand).
Compared structures
- 1XPU · Structural mechanism of inhibition of the Rho transcription termination factor by the… · the same entry in another collection · chain F against F, TM-score 1.00
- P22869 · AlphaFold monomer V2.0 prediction for methane monooxygenase component a alpha chain… · a predicted model of the same protein · chain E against A, TM-score 0.29
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 P22869
- Elsewhere: RCSB PDB 1XPU · PDBe 1XPU · UniProt P22869
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