Research workbench
Thermus thermophilus RNA polymerase transcription initiation complex containing a template-strand purine at position TSS-2, UpA RNA primer and CMPcPP
Analyse Thermus thermophilus RNA polymerase transcription initiation complex containing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EH0
- Type
- protein + DNA + RNA
- Length
- 3,537 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.808
- Source
- Thermus thermophilus HB8; SYNTHETIC CONSTRUCT
- Molecule
- DNA-directed RNA polymerase subunit alpha; DNA-directed RNA polymerase subunit beta…
- EC
- 2.7.7.6
- UniProt
- Q5SHR6, Q8RQE9, Q8RQE8, Q8RQE7, Q5SKW1
- Ligands
- 2TM, MG, ZN
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · resolution 2.808 · 9 distinct chains · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 231 | 22% helix, 40% strand | Q5SHR6 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 224 | 22% helix, 43% strand | Q5SHR6 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1112 | 29% helix, 27% strand | Q8RQE9 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1486 | 37% helix, 24% strand | Q8RQE8 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 94 | 50% helix, 12% strand | Q8RQE7 |
| F | RNA polymerase sigma factor SigA | protein | 346 | 70% helix, 2% strand | Q5SKW1 |
| G | DNA (27-mer) | dna | 25 | — | — |
| H | DNA (5'-D(*CP*C*TP*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*TP*AP*AP*AP*G)-3') | dna | 17 | — | — |
| I | RNA (5'-R(*UP*A)-3') | rna | 2 | — | — |
Ligands and binding sites
- 2TM · 5'-O-[(S)-hydroxy{[(s)-hydroxy(phosphonooxy) phosphoryl]methyl}phosphoryl]cytidine · ligand · chains C, D, H, I
- MG · Magnesium ion · metal · 5 copies · chains B, D, I, F
- ZN · Zinc ion · metal · 2 copies · chains D
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 | 1034 | 0.85 | 0.86 | 90 | empty |
| 2 | 922 | 0.85 | 0.87 | 79 | empty |
| 3 | 482 | 0.85 | 0.92 | 70 | empty |
| 4 | 716 | 0.82 | 0.86 | 87 | empty |
| 5 | 589 | 0.80 | 0.85 | 57 | empty |
Interfaces
21 interfaces between chains.
- C–D · 8900 Ų buried · 129 hydrogen bonds · protein-protein
- D–F · 4032 Ų buried · 51 hydrogen bonds · protein-protein
- C–F · 2527 Ų buried · 25 hydrogen bonds · protein-protein
- D–E · 2383 Ų buried · 40 hydrogen bonds · protein-protein
- A–C · 2079 Ų buried · 46 hydrogen bonds · protein-protein
Compared structures
- 7EH0 · Thermus thermophilus RNA polymerase transcription initiation complex containing a… · the same entry in another collection · chain H against H, TM-score 1.00
- Q8RQE9 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta (Q8RQE9) · a predicted model of the same protein · chain C against A, TM-score 0.98
- Q8RQE8 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta' (Q8RQE8) · a predicted model of the same protein · chain D against A, TM-score 0.98
- Q8RQE7 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit omega (Q8RQE7) · a predicted model of the same protein · chain E against A, TM-score 0.98
- Q5SHR6 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit alpha (Q5SHR6) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q5SHR6
- Every structure of UniProt Q8RQE9
- Every structure of UniProt Q8RQE8
- Every structure of UniProt Q8RQE7
- Every structure of UniProt Q5SKW1
- Elsewhere: RCSB PDB 7EH0 · PDBe 7EH0 · UniProt Q5SHR6 · UniProt Q8RQE9 · UniProt Q8RQE8 · UniProt Q8RQE7 · UniProt Q5SKW1
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