MolNFT v1 · #169403 · protein + DNA + RNA
Cryoem structure of E. COLI rho-dependent transcription pre- termination complex bound with nusg
6XAV · Transcription TERMINATION/ANTITERMINATION protein nusg: “Cryoem structure of E. COLI rho-dependent transcription pre- termination complex bound with nusg”. Electron microscopy, 2 ligands (ZN, MG), 20 pockets (best druggability…
- PDB
- 6XAV
- Type
- protein + DNA + RNA
- Length
- 5,869 residues
- Chains
- 16
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Transcription TERMINATION/ANTITERMINATION protein nusg; DNA (29-mer); RNA (18-mer)…
- EC
- 2.7.7.6, 3.6.4.-
- UniProt
- P0AFG0, P0A800, P0A7Z4, P0A8V2, P0A8T7, P0AFF6, P0AG30
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 15 distinct chains · 34% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Transcription TERMINATION/ANTITERMINATION protein nusg | protein | 95 | 37% helix, 19% strand | P0AFG0 |
| N | DNA (29-mer) | dna | 27 | — | — |
| T | DNA (29-mer) | dna | 29 | — | — |
| R | RNA (18-mer) | rna | 10 | — | — |
| W | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 55 | 51% helix, 0% strand | P0A800 |
| K | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 279 | 24% helix, 27% strand | P0A7Z4 |
| H | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 218 | 17% helix, 35% strand | P0A7Z4 |
| I | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1304 | 28% helix, 22% strand | P0A8V2 |
| J | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1338 | 36% helix, 15% strand | P0A8T7 |
| G | Transcription TERMINATION/ANTITERMINATION protein nusa | protein | 166 | 28% helix, 27% strand | P0AFF6 |
| C | Transcription termination factor rho (EC 3.6.4.-) | protein | 413 | 41% helix, 20% strand | P0AG30 |
| A | Transcription termination factor rho (EC 3.6.4.-) | protein | 353 | 40% helix, 22% strand | P0AG30 |
| B | Transcription termination factor rho (EC 3.6.4.-) | protein | 407 | 42% helix, 21% strand | P0AG30 |
| D, E | Transcription termination factor rho (EC 3.6.4.-) | protein | 415 | 41% helix, 19% strand | P0AG30 |
| F | Transcription termination factor rho (EC 3.6.4.-) | protein | 345 | 37% helix, 22% strand | P0AG30 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1042 | 0.86 | 0.87 | 98 | empty |
| 2 | 984 | 0.85 | 0.86 | 86 | empty |
| 3 | 737 | 0.84 | 0.88 | 84 | empty |
| 4 | 863 | 0.81 | 0.83 | 74 | empty |
| 5 | 1035 | 0.81 | 0.82 | 84 | empty |
Interfaces
38 interfaces between chains.
- I–J · 8695 Ų buried · 101 hydrogen bonds · protein-protein
- K–H · 1952 Ų buried · 11 hydrogen bonds · protein-protein
- K–I · 1883 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1500 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 1433 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6XAV · CryoEM Structure of E. coli Rho-dependent Transcription Pre-termination Complex bound… · the same entry in another collection · chain F against F, TM-score 1.00
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 P0AFG0
- Every structure of UniProt P0A800
- Every structure of UniProt P0A7Z4
- Every structure of UniProt P0A8V2
- Every structure of UniProt P0A8T7
- Every structure of UniProt P0AFF6
- Every structure of UniProt P0AG30
- Elsewhere: RCSB PDB 6XAV · PDBe 6XAV · UniProt P0AFG0 · UniProt P0A800 · UniProt P0A7Z4 · UniProt P0A8V2 · UniProt P0A8T7 · UniProt P0AFF6 · UniProt P0AG30
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