Research workbench
Pseudo-atomic model of the RNA polymerase lambda-based antitermination complex solved by cryo-EM
Analyse Pseudo-atomic model of the RNA polymerase lambda-based antitermination complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MS0
- Type
- protein + DNA + RNA
- Length
- 4,253 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Antitermination protein N; Nascent RNA; DNA-directed RNA polymerase subunit alpha…
- EC
- 2.7.7.6
- UniProt
- P03045, P0A7Z4, P0A8V2, P0A8T7, P0A7R5, P0AFG0, P0A780, P0AFF6, P0A800
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 13 distinct chains · 27% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| N | Antitermination protein N | protein | 85 | 46% helix, 0% strand | P03045 |
| R | Nascent RNA | rna | 29 | — | — |
| A, B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 235 | 15% helix, 28% strand | P0A7Z4 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1291 | 24% helix, 16% strand | P0A8V2 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1364 | 24% helix, 11% strand | P0A8T7 |
| E | 30S ribosomal protein S10 | protein | 100 | 26% helix, 32% strand | P0A7R5 |
| F | Transcription TERMINATION/ANTITERMINATION protein nusg | protein | 181 | 14% helix, 20% strand | P0AFG0 |
| H | RNA transcription bubble | rna | 14 | — | — |
| I | Dnai | dna | 27 | — | — |
| J | Dnaii | dna | 39 | — | — |
| L | Transcription antitermination protein nusb | protein | 139 | 62% helix, 0% strand | P0A780 |
| M | Transcription TERMINATION/ANTITERMINATION protein nusa | protein | 425 | 39% helix, 16% strand | P0AFF6 |
| O | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 89 | 39% helix, 0% strand | P0A800 |
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 | 1123 | 0.83 | 0.84 | 151 | empty |
| 2 | 481 | 0.82 | 0.89 | 87 | empty |
| 3 | 965 | 0.82 | 0.84 | 110 | empty |
| 4 | 422 | 0.82 | 0.90 | 81 | empty |
| 5 | 658 | 0.81 | 0.86 | 89 | empty |
Interfaces
29 interfaces between chains.
- C–D · 3264 Ų buried · 13 hydrogen bonds · protein-protein
- I–J · 1238 Ų buried · 100 hydrogen bonds · nucleic-nucleic
- N–M · 792 Ų buried · 0 hydrogen bonds · protein-protein
- D–O · 761 Ų buried · 2 hydrogen bonds · protein-protein
- D–J · 758 Ų buried · 22 hydrogen bonds · protein-nucleic
Compared structures
- 5MS0 · pseudo-atomic model of the RNA polymerase lambda-based antitermination complex solved by… · the same entry in another collection · chain O against O, 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 P03045
- Every structure of UniProt P0A7Z4
- Every structure of UniProt P0A8V2
- Every structure of UniProt P0A8T7
- Every structure of UniProt P0A7R5
- Every structure of UniProt P0AFG0
- Every structure of UniProt P0A780
- Every structure of UniProt P0AFF6
- Every structure of UniProt P0A800
- Elsewhere: RCSB PDB 5MS0 · PDBe 5MS0 · UniProt P03045 · UniProt P0A7Z4 · UniProt P0A8V2 · UniProt P0A8T7 · UniProt P0A7R5 · UniProt P0AFG0 · UniProt P0A780 · UniProt P0AFF6 · UniProt P0A800
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