Research workbench
Rho transcription termination factor bound to RNA and ADP-BEF3
Analyse Rho transcription termination factor bound to RNA and ADP-BEF3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ICE
- Type
- protein + RNA
- Length
- 2,438 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcription termination factor rho; 5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3'
- EC
- 3.6.1.-
- UniProt
- P0AG30
- Ligands
- ADP, BEF, SPD, MG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 7 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcription termination factor rho (EC 3.6.1.-) | protein | 398 | 40% helix, 20% strand | P0AG30 |
| B | Transcription termination factor rho (EC 3.6.1.-) | protein | 408 | 44% helix, 20% strand | P0AG30 |
| C | Transcription termination factor rho (EC 3.6.1.-) | protein | 413 | 39% helix, 20% strand | P0AG30 |
| D | Transcription termination factor rho (EC 3.6.1.-) | protein | 410 | 40% helix, 20% strand | P0AG30 |
| E | Transcription termination factor rho (EC 3.6.1.-) | protein | 407 | 41% helix, 20% strand | P0AG30 |
| F | Transcription termination factor rho (EC 3.6.1.-) | protein | 396 | 38% helix, 21% strand | P0AG30 |
| G | 5'-R(P*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*UP*U)-3' | rna | 6 | — | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 6 copies · chains A, B, C, D, E, F
- BEF · Beryllium trifluoride ion · ligand · 6 copies · chains A, B, C, D, E, F
- SPD · Spermidine · ligand · 2 copies · chains E, A, B, C, G
- 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, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 945 | 0.83 | 0.85 | 91 | empty |
| 2 | 685 | 0.79 | 0.83 | 81 | ADP, BEF |
| 3 | 681 | 0.77 | 0.83 | 70 | ADP, MG, BEF |
| 4 | 604 | 0.77 | 0.83 | 71 | ADP, MG, BEF |
| 5 | 572 | 0.76 | 0.83 | 67 | ADP, MG, BEF |
Interfaces
12 interfaces between chains.
- A–B · 1730 Ų buried · 27 hydrogen bonds · protein-protein
- D–E · 1722 Ų buried · 39 hydrogen bonds · protein-protein
- C–D · 1718 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 1672 Ų buried · 26 hydrogen bonds · protein-protein
- A–F · 1610 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 83 modified (engineered).
Compared structures
- 3ICE · Rho transcription termination factor bound to RNA and ADP-BeF3 · the same entry in another collection · chain G against G, TM-score 1.00
- P0AG30 · AlphaFold monomer V2.0 prediction for transcription termination factor rho (P0AG30) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P0AG30
- Elsewhere: RCSB PDB 3ICE · PDBe 3ICE · UniProt P0AG30
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