Research workbench
Escherichia COLI RNA polymerase and RRNBP1 promoter pre-open complex with DKSA/PPGPP
Analyse Escherichia COLI RNA polymerase and RRNBP1 promoter pre-open complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KHE
- Type
- protein + DNA
- Length
- 3,950 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
- P0A7Z4, P0A8V2, P0A8T7, P0A800, P00579, P0ABS1
- Ligands
- 1N7, G4P, ZN, MG
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 9 distinct chains · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 230 | 23% helix, 39% strand | P0A7Z4 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 228 | 21% helix, 39% strand | P0A7Z4 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1340 | 31% helix, 23% strand | P0A8V2 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1363 | 37% helix, 16% strand | P0A8T7 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 76 | 61% helix, 0% strand | P0A800 |
| F | RNA polymerase sigma factor rpod | protein | 471 | 69% helix, 1% strand | P00579 |
| X | DNA (54-mer) | dna | 54 | — | — |
| Y | DNA (46-mer) | dna | 46 | — | — |
| M | RNA polymerase-binding transcription factor dksa | protein | 142 | 65% helix, 1% strand | P0ABS1 |
Ligands and binding sites
- 1N7 · Chapso · ligand · 4 copies · chains A, C, D, F
- G4P · Guanosine-5',3'-tetraphosphate · ligand · 2 copies · chains D, E, M
- ZN · Zinc ion · metal · 3 copies · chains D, M
- MG · Magnesium ion · metal · chains D, M
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 | 792 | 0.81 | 0.84 | 63 | empty |
| 2 | 458 | 0.80 | 0.88 | 44 | empty |
| 3 | 832 | 0.79 | 0.82 | 68 | empty |
| 4 | 753 | 0.78 | 0.83 | 58 | empty |
| 5 | 532 | 0.78 | 0.85 | 52 | empty |
Interfaces
18 interfaces between chains.
- C–D · 8301 Ų buried · 92 hydrogen bonds · protein-protein
- D–M · 2508 Ų buried · 13 hydrogen bonds · protein-protein
- D–F · 2485 Ų buried · 12 hydrogen bonds · protein-protein
- X–Y · 2118 Ų buried · 171 hydrogen bonds · nucleic-nucleic
- A–B · 2096 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7KHE · Escherichia coli RNA polymerase and rrnBP1 promoter pre-open complex with DksA/ppGpp · the same entry in another collection · chain M against M, TM-score 1.00
- P0ABS1 · AlphaFold monomer V2.0 prediction for RNA polymerase-binding transcription factor dksa… · a predicted model of the same protein · chain M against A, TM-score 0.91
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 P0A7Z4
- Every structure of UniProt P0A8V2
- Every structure of UniProt P0A8T7
- Every structure of UniProt P0A800
- Every structure of UniProt P00579
- Every structure of UniProt P0ABS1
- Elsewhere: RCSB PDB 7KHE · PDBe 7KHE · UniProt P0A7Z4 · UniProt P0A8V2 · UniProt P0A8T7 · UniProt P0A800 · UniProt P00579 · UniProt P0ABS1
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