Research workbench
Cryo-EM structure of thermus thermophilus reiterative transcription complex with 11NT oligo-G RNA
Analyse Cryo-EM structure of thermus thermophilus reiterative transcription complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RDQ
- Type
- protein + DNA + RNA
- Length
- 3,441 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- 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
- MG, ZN
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 9 distinct chains · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 226 | 22% helix, 38% strand | Q5SHR6 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 222 | 23% helix, 41% strand | Q5SHR6 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1111 | 28% helix, 27% strand | Q8RQE9 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1366 | 39% helix, 21% strand | Q8RQE8 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 94 | 51% helix, 12% strand | Q8RQE7 |
| F | RNA polymerase sigma factor siga | protein | 349 | 67% helix, 2% strand | Q5SKW1 |
| H | DNA (31-mer) nontemplate strand | dna | 31 | — | — |
| G | DNA (31-mer) template strand | dna | 31 | — | — |
| I | RNA (5'-R(P*GP*GP*GP*GP*GP*GP*GP*GP*GP*GP*G)-3') | rna | 11 | — | — |
Ligands and binding sites
- 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 | 594 | 0.85 | 0.91 | 67 | empty |
| 2 | 1039 | 0.84 | 0.85 | 85 | empty |
| 3 | 810 | 0.84 | 0.86 | 80 | MG |
| 4 | 439 | 0.84 | 0.92 | 58 | empty |
| 5 | 883 | 0.83 | 0.85 | 108 | empty |
Interfaces
22 interfaces between chains.
- C–D · 8816 Ų buried · 94 hydrogen bonds · protein-protein
- D–F · 3968 Ų buried · 37 hydrogen bonds · protein-protein
- D–E · 2459 Ų buried · 26 hydrogen bonds · protein-protein
- C–F · 2092 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 2019 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 7RDQ · Cryo-EM structure of Thermus thermophilus reiterative transcription complex with 11nt… · the same entry in another collection · chain I against I, TM-score 1.00
- 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 0.97
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 Q5SHR6
- Every structure of UniProt Q8RQE9
- Every structure of UniProt Q8RQE8
- Every structure of UniProt Q8RQE7
- Every structure of UniProt Q5SKW1
- Elsewhere: RCSB PDB 7RDQ · PDBe 7RDQ · UniProt Q5SHR6 · UniProt Q8RQE9 · UniProt Q8RQE8 · UniProt Q8RQE7 · UniProt Q5SKW1
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