MolNFT v1 · #18627 · protein + DNA
X-ray crystal structure of the rho transcription termination factor in complex with single stranded DNA
1PV4 · 5'-D(P*CP*C)-3': “X-ray crystal structure of the rho transcription termination factor in complex with single stranded DNA”. X-ray diffraction, 20 pockets (best druggability 0.83). MolNFT v1 #18627 on GenesisL1: 3D structure, binding…
- PDB
- 1PV4
- Type
- protein + DNA
- Length
- 2,407 residues
- Chains
- 11
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(P*CP*C)-3'; Transcription termination factor rho
- UniProt
- P0AG30
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G, H, J, K, L | 5'-D(P*CP*C)-3' | dna | 2 | — | — |
| A, C, D, F | Transcription termination factor rho | protein | 408 | 40% helix, 19% strand | P0AG30 |
| B | Transcription termination factor rho | protein | 358 | 40% helix, 22% strand | P0AG30 |
| E | Transcription termination factor rho | protein | 407 | 41% helix, 20% strand | P0AG30 |
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 | 1074 | 0.83 | 0.84 | 100 | empty |
| 2 | 1070 | 0.83 | 0.84 | 96 | empty |
| 3 | 1198 | 0.82 | 0.83 | 101 | empty |
| 4 | 995 | 0.80 | 0.82 | 85 | empty |
| 5 | 1088 | 0.79 | 0.81 | 90 | empty |
Interfaces
10 interfaces between chains.
- B–C · 1577 Ų buried · 28 hydrogen bonds · protein-protein
- D–E · 1566 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 1552 Ų buried · 27 hydrogen bonds · protein-protein
- E–F · 1536 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 1113 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 93 modified (engineered).
Compared structures
- 1PV4 · X-ray crystal structure of the Rho transcription termination factor in complex with… · 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 1PV4 · PDBe 1PV4 · UniProt P0AG30
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.