Research workbench
Thermus thermophilus transcription initiation complex containing a template-strand pyrimidine at position TSS-2 and GpG RNA primer
Analyse Thermus thermophilus transcription initiation complex containing a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EH2
- Type
- protein + DNA + RNA
- Length
- 7,066 residues
- Chains
- 18
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.34
- 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
- ZN, MG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · resolution 3.34 · 12 distinct chains · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 229 | 22% helix, 40% strand | Q5SHR6 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 222 | 20% helix, 41% strand | Q5SHR6 |
| C, M | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1111 | 30% helix, 27% strand | Q8RQE9 |
| D, N | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1486 | 37% helix, 24% strand | Q8RQE8 |
| E, O | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 94 | 52% helix, 11% strand | Q8RQE7 |
| F | RNA polymerase sigma factor SigA | protein | 346 | 69% helix, 1% strand | Q5SKW1 |
| K | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 227 | 20% helix, 39% strand | Q5SHR6 |
| L | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 225 | 20% helix, 42% strand | Q5SHR6 |
| P | RNA polymerase sigma factor SigA | protein | 347 | 68% helix, 1% strand | Q5SKW1 |
| G, J | DNA (27-mer) | dna | 25 | — | — |
| H, Q | DNA (5'-D(*CP*C*TP*GP*CP*AP*TP*CP*CP*GP*TP*GP*AP*GP*CP*CP*TP*AP*G)-3') | dna | 17 | — | — |
| I, R | RNA (5'-R(*GP*G)-3') | rna | 2 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains D, N
- MG · Magnesium ion · metal · 3 copies · chains D, I, L, N, R
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 | 1133 | 0.86 | 0.87 | 105 | empty |
| 2 | 1123 | 0.86 | 0.87 | 97 | empty |
| 3 | 1070 | 0.84 | 0.85 | 91 | empty |
| 4 | 1133 | 0.84 | 0.85 | 99 | empty |
| 5 | 540 | 0.84 | 0.90 | 66 | empty |
Interfaces
44 interfaces between chains.
- C–D · 9031 Ų buried · 127 hydrogen bonds · protein-protein
- M–N · 8977 Ų buried · 125 hydrogen bonds · protein-protein
- N–P · 4070 Ų buried · 47 hydrogen bonds · protein-protein
- D–F · 4036 Ų buried · 53 hydrogen bonds · protein-protein
- M–P · 2556 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 7EH2 · Thermus thermophilus transcription initiation complex containing a template-strand… · the same entry in another collection · chain Q against Q, 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 Q5SHR6
- Every structure of UniProt Q8RQE9
- Every structure of UniProt Q8RQE8
- Every structure of UniProt Q8RQE7
- Every structure of UniProt Q5SKW1
- Elsewhere: RCSB PDB 7EH2 · PDBe 7EH2 · UniProt Q5SHR6 · UniProt Q8RQE9 · UniProt Q8RQE8 · UniProt Q8RQE7 · UniProt Q5SKW1
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