Research workbench
Rho transcription termination factor bound to RU8 and 5 ADP-BEF3 molecules
Analyse Rho transcription termination factor bound to RU8 and 5 ADP-BEF3 molecules in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JJL
- Type
- protein + RNA
- Length
- 2,417 residues
- Chains
- 7
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcription termination factor rho; RU12: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*U)-3')
- EC
- 3.6.4.-
- UniProt
- P0AG32
- Ligands
- ADP, BEF, MG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 7 distinct chains · 42% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transcription termination factor rho (EC 3.6.4.-) | protein | 396 | 42% helix, 20% strand | P0AG32 |
| B | Transcription termination factor rho (EC 3.6.4.-) | protein | 409 | 42% helix, 20% strand | P0AG32 |
| C | Transcription termination factor rho (EC 3.6.4.-) | protein | 415 | 42% helix, 21% strand | P0AG32 |
| D | Transcription termination factor rho (EC 3.6.4.-) | protein | 406 | 43% helix, 20% strand | P0AG32 |
| E | Transcription termination factor rho (EC 3.6.4.-) | protein | 381 | 44% helix, 19% strand | P0AG32 |
| F | Transcription termination factor rho (EC 3.6.4.-) | protein | 402 | 42% helix, 22% strand | P0AG32 |
| G | RU12: RNA (5'-R(P*UP*UP*UP*UP*UP*UP*U)-3') | rna | 8 | — | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 5 copies · chains A, B, C, D, E, F
- BEF · Beryllium trifluoride ion · ligand · 5 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 5 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1167 | 0.86 | 0.87 | 139 | ADP, MG, BEF |
| 2 | 857 | 0.82 | 0.84 | 89 | empty |
| 3 | 511 | 0.77 | 0.84 | 63 | ADP, MG, BEF |
| 4 | 553 | 0.75 | 0.83 | 66 | ADP, MG, BEF |
| 5 | 517 | 0.75 | 0.83 | 56 | ADP, MG, BEF |
Interfaces
12 interfaces between chains.
- A–B · 1721 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 1708 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 1685 Ų buried · 31 hydrogen bonds · protein-protein
- D–E · 1664 Ų buried · 29 hydrogen bonds · protein-protein
- A–F · 1400 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 88 modified (engineered).
Compared structures
- 5JJL · Rho transcription termination factor bound to rU8 and 5 ADP-BeF3 molecules · the same entry in another collection · chain G against G, TM-score 1.00
- P0AG32 · AlphaFold monomer V2.0 prediction for transcription termination factor rho (P0AG32) · a predicted model of the same protein · chain C 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 P0AG32
- Elsewhere: RCSB PDB 5JJL · PDBe 5JJL · UniProt P0AG32
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