MolNFT v1 · #179832 · protein + DNA
Escherichia COLI RNA polymerase and RRNBP1 promoter pre-open complex with DKSA/PPGPP
7KHE: “Escherichia COLI RNA polymerase and RRNBP1 promoter pre-open complex with DKSA/PPGPP”. Electron microscopy, 4 ligands (1N7, G4P, ZN). MolNFT v1 #179832 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7KHE
- Type
- protein + DNA
- Length
- 3,950 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- UniProt
- P0A7Z4, P0A8V2, P0A8T7, P0A800, P00579, P0ABS1
- Ligands
- 1N7, G4P, ZN, MG
Structure
electron microscopy · 9 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | — | protein | 230 | — | P0A7Z4 |
| B | — | protein | 228 | — | P0A7Z4 |
| C | — | protein | 1340 | — | P0A8V2 |
| D | — | protein | 1363 | — | P0A8T7 |
| E | — | protein | 76 | — | P0A800 |
| F | — | protein | 471 | — | P00579 |
| X | — | dna | 54 | — | — |
| Y | — | dna | 46 | — | — |
| M | — | protein | 142 | — | 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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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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