Research workbench
X-ray crystal structure of bacterial RNA polymerase and pyrbi promoter complex
Analyse X-ray crystal structure of bacterial RNA polymerase and pyrbi promoter complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6P70
- Type
- protein + DNA
- Length
- 3,525 residues
- Chains
- 8
- Method
- x-ray diffraction
- 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
- Q9Z9H6, Q8RQE9, Q8RQE8, A0A1J1EUF1, Q72L95
- Ligands
- MG, ZN
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 8 distinct chains · 36% helix, 24% 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 | Q9Z9H6 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 222 | 20% helix, 41% strand | Q9Z9H6 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1111 | 30% helix, 26% 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 | 49% helix, 11% strand | A0A1J1EUF1 |
| F | RNA polymerase sigma factor siga | protein | 346 | 68% helix, 1% strand | Q72L95 |
| G | DNA (5'- D(P*TP*CP*CP*CP*GP*GP*CP*AP*AP*AP*TP*TP*GP*TP*CP*CP*G)-3') | dna | 18 | — | — |
| H | DNA (5'- D(*TP*AP*TP*AP*AP*TP*CP*GP*AP*TP*CP*TP*TP*TP*GP*CP*CP*GP*GP*G)-3') | dna | 22 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains B, D, F, G
- 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 | 1105 | 0.86 | 0.87 | 95 | empty |
| 2 | 475 | 0.85 | 0.92 | 61 | MG |
| 3 | 1142 | 0.84 | 0.85 | 95 | empty |
| 4 | 568 | 0.81 | 0.87 | 65 | empty |
| 5 | 636 | 0.78 | 0.83 | 73 | empty |
Interfaces
18 interfaces between chains.
- C–D · 9048 Ų buried · 130 hydrogen bonds · protein-protein
- D–F · 4205 Ų buried · 60 hydrogen bonds · protein-protein
- C–F · 2546 Ų buried · 28 hydrogen bonds · protein-protein
- D–E · 2397 Ų buried · 37 hydrogen bonds · protein-protein
- A–C · 2083 Ų buried · 42 hydrogen bonds · protein-protein
Compared structures
- 6P70 · X-ray crystal structure of bacterial RNA polymerase and pyrBI promoter complex · the same entry in another collection · chain H against H, TM-score 1.00
- Q72L95 · AlphaFold monomer V2.0 prediction for RNA polymerase sigma factor siga (Q72L95) · a predicted model of the same protein · chain F against A, TM-score 0.98
- Q9Z9H6 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit alpha (Q9Z9H6) · a predicted model of the same protein · chain A 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 Q9Z9H6
- Every structure of UniProt Q8RQE9
- Every structure of UniProt Q8RQE8
- Every structure of UniProt A0A1J1EUF1
- Every structure of UniProt Q72L95
- Elsewhere: RCSB PDB 6P70 · PDBe 6P70 · UniProt Q9Z9H6 · UniProt Q8RQE9 · UniProt Q8RQE8 · UniProt A0A1J1EUF1 · UniProt Q72L95
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