Research workbench
Q21 transcription antitermination complex: loading complex
Analyse Q21 transcription antitermination complex: loading complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6P18
- Type
- protein + DNA + RNA
- Length
- 3,949 residues
- Chains
- 11
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (67-mer) fragment carrying phage-21 pr' promoter and pause element, nontemplate…
- EC
- 2.7.7.6
- UniProt
- P0A7Z4, P0A8V2, P0A8T7, P0A800, P00579, Q9XJQ6
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 11 distinct chains · 37% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | DNA (67-mer) fragment carrying phage-21 pr' promoter and pause element, nontemplate strand | dna | 56 | — | — |
| 2 | DNA (67-mer) fragment carrying phage-21 pr' promoter and pause element, template strand | dna | 56 | — | — |
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 230 | 23% helix, 32% strand | P0A7Z4 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 228 | 20% helix, 35% strand | P0A7Z4 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1340 | 30% helix, 24% strand | P0A8V2 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1327 | 37% helix, 16% strand | P0A8T7 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 75 | 68% helix, 0% strand | P0A800 |
| F | RNA polymerase sigma factor rpod | protein | 325 | 67% helix, 1% strand | P00579 |
| P | Q protein | protein | 145 | 59% helix, 3% strand | Q9XJQ6 |
| Q | Q protein | protein | 156 | 59% helix, 1% strand | Q9XJQ6 |
| R | RNA (5'-R(P*UP*GP*GP*GP*AP*GP*AP*GP*GP*UP*A)-3') | rna | 11 | — | — |
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 | 897 | 0.86 | 0.89 | 105 | empty |
| 2 | 787 | 0.82 | 0.85 | 61 | empty |
| 3 | 819 | 0.82 | 0.85 | 76 | empty |
| 4 | 949 | 0.80 | 0.82 | 89 | empty |
| 5 | 108 | 0.75 | 0.94 | 20 | empty |
Interfaces
29 interfaces between chains.
- C–D · 8114 Ų buried · 81 hydrogen bonds · protein-protein
- A–B · 2036 Ų buried · 8 hydrogen bonds · protein-protein
- 1–2 · 1911 Ų buried · 137 hydrogen bonds · nucleic-nucleic
- A–C · 1764 Ų buried · 19 hydrogen bonds · protein-protein
- D–F · 1735 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6P18 · Q21 transcription antitermination complex: loading complex · the same entry in another collection · chain R against R, TM-score 1.00
- P0A8V2 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta (P0A8V2) · a predicted model of the same protein · chain C against A, TM-score 0.97
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 P0A7Z4
- Every structure of UniProt P0A8V2
- Every structure of UniProt P0A8T7
- Every structure of UniProt P0A800
- Every structure of UniProt P00579
- Every structure of UniProt Q9XJQ6
- Elsewhere: RCSB PDB 6P18 · PDBe 6P18 · UniProt P0A7Z4 · UniProt P0A8V2 · UniProt P0A8T7 · UniProt P0A800 · UniProt P00579 · UniProt Q9XJQ6
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