Research workbench
X-ray crystal structure of rho transcription termination factor in complex with ssrna substrate and anppnp
Analyse X-ray crystal structure of rho transcription termination factor in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PVO
- Type
- protein + RNA
- Length
- 2,407 residues
- Chains
- 11
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-R(P*UP*C)-3'; Transcription termination factor rho
- UniProt
- P0AG30
- Ligands
- ANP
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G, H, J, K, L | 5'-R(P*UP*C)-3' | rna | 2 | — | — |
| A, C, D, F | Transcription termination factor rho | protein | 408 | 40% helix, 20% strand | P0AG30 |
| B | Transcription termination factor rho | protein | 358 | 39% helix, 20% strand | P0AG30 |
| E | Transcription termination factor rho | protein | 407 | 39% helix, 20% strand | P0AG30 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1148 | 0.83 | 0.84 | 92 | ANP |
| 2 | 1095 | 0.83 | 0.84 | 103 | ANP |
| 3 | 1075 | 0.82 | 0.83 | 99 | ANP |
| 4 | 992 | 0.80 | 0.82 | 79 | ANP |
| 5 | 1177 | 0.79 | 0.81 | 86 | ANP |
Interfaces
10 interfaces between chains.
- C–D · 1620 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 1618 Ų buried · 32 hydrogen bonds · protein-protein
- D–E · 1603 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 1591 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1077 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 1PVO · X-ray crystal structure of Rho transcription termination factor in complex with ssRNA… · the same entry in another collection · chain F against F, 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 1PVO · PDBe 1PVO · UniProt P0AG30
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.