Research workbench
X-ray crystal structure of bacterial RNA polymerase and pyrg promoter complex
Analyse X-ray crystal structure of bacterial RNA polymerase and pyrg promoter complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VOI
- 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
- Q72I32, Q8RQE9, Q8RQE8, Q8RQE7, Q5SKW1
- 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 | Q72I32 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 222 | 23% helix, 42% strand | Q72I32 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1111 | 30% 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 | 48% helix, 11% strand | Q8RQE7 |
| F | RNA polymerase sigma factor siga | protein | 346 | 69% helix, 2% strand | Q5SKW1 |
| G | Pyrg promoter | dna | 18 | — | — |
| H | Pyrg promoter | dna | 22 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains D, B, 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 | 1072 | 0.86 | 0.87 | 98 | empty |
| 2 | 1025 | 0.85 | 0.86 | 93 | empty |
| 3 | 397 | 0.83 | 0.91 | 52 | MG |
| 4 | 1022 | 0.79 | 0.81 | 106 | empty |
| 5 | 496 | 0.79 | 0.86 | 58 | empty |
Interfaces
18 interfaces between chains.
- C–D · 9008 Ų buried · 130 hydrogen bonds · protein-protein
- D–F · 4079 Ų buried · 59 hydrogen bonds · protein-protein
- C–F · 2569 Ų buried · 28 hydrogen bonds · protein-protein
- D–E · 2392 Ų buried · 38 hydrogen bonds · protein-protein
- A–C · 2048 Ų buried · 36 hydrogen bonds · protein-protein
Compared structures
- 5VOI · X-ray crystal structure of bacterial RNA polymerase and pyrG promoter complex · the same entry in another collection · chain H against H, 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
- Q72I32 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit alpha (Q72I32) · 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 Q72I32
- Every structure of UniProt Q8RQE9
- Every structure of UniProt Q8RQE8
- Every structure of UniProt Q8RQE7
- Every structure of UniProt Q5SKW1
- Elsewhere: RCSB PDB 5VOI · PDBe 5VOI · UniProt Q72I32 · UniProt Q8RQE9 · UniProt Q8RQE8 · UniProt Q8RQE7 · UniProt Q5SKW1
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