MolNFT v1 · #96449 · protein
X-ray crystal structure of escherichia COLI SIGMA70 holoenzyme in complex with guanosine tetraphosphate (ppgpp)
4JK1 · Escherichia COLI RNA polymerase alpha subunit: “X-ray crystal structure of escherichia COLI SIGMA70 holoenzyme in complex with guanosine tetraphosphate…”. X-ray diffraction, 2 ligands (G4P, ZN), 20 pockets (best druggability 0.85).…
- PDB
- 4JK1
- Type
- protein
- Length
- 7,121 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Escherichia COLI RNA polymerase alpha subunit; Escherichia COLI RNA polymerase beta…
- EC
- 2.7.7.6
- UniProt
- P0A7Z4, P0A8V2, P0A8T7, H0QDQ9, P00579
- Ligands
- G4P, ZN
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 10 distinct chains · 38% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Escherichia COLI RNA polymerase alpha subunit (EC 2.7.7.6) | protein | 323 | 25% helix, 24% strand | P0A7Z4 |
| B | Escherichia COLI RNA polymerase alpha subunit (EC 2.7.7.6) | protein | 221 | 19% helix, 35% strand | P0A7Z4 |
| C, H | Escherichia COLI RNA polymerase beta subunit (EC 2.7.7.6) | protein | 1335 | 27% helix, 18% strand | P0A8V2 |
| D, I | Escherichia COLI RNA polymerase beta' subunit (EC 2.7.7.6) | protein | 1160 | 38% helix, 10% strand | P0A8T7 |
| E | Escherichia COLI RNA polymerase omega subunit (EC 2.7.7.6) | protein | 90 | 62% helix, 0% strand | H0QDQ9 |
| X | Escherichia COLI RNA polymerase SIGMA70 subunit | protein | 517 | 64% helix, 1% strand | P00579 |
| F | Escherichia COLI RNA polymerase alpha subunit (EC 2.7.7.6) | protein | 229 | 19% helix, 31% strand | P0A7Z4 |
| G | Escherichia COLI RNA polymerase alpha subunit (EC 2.7.7.6) | protein | 217 | 19% helix, 37% strand | P0A7Z4 |
| J | Escherichia COLI RNA polymerase omega subunit (EC 2.7.7.6) | protein | 76 | 61% helix, 0% strand | H0QDQ9 |
| Y | Escherichia COLI RNA polymerase SIGMA70 subunit | protein | 458 | 67% helix, 1% strand | P00579 |
Ligands and binding sites
- G4P · Guanosine-5',3'-tetraphosphate · ligand · chains D, E
- ZN · Zinc ion · metal · 4 copies · chains D, I
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 | 874 | 0.85 | 0.87 | 103 | empty |
| 2 | 670 | 0.84 | 0.88 | 76 | empty |
| 3 | 1075 | 0.79 | 0.80 | 110 | empty |
| 4 | 847 | 0.78 | 0.81 | 92 | empty |
| 5 | 347 | 0.78 | 0.89 | 50 | empty |
Interfaces
22 interfaces between chains.
- H–I · 8148 Ų buried · 97 hydrogen bonds · protein-protein
- C–D · 8032 Ų buried · 101 hydrogen bonds · protein-protein
- D–X · 3631 Ų buried · 42 hydrogen bonds · protein-protein
- I–Y · 2847 Ų buried · 30 hydrogen bonds · protein-protein
- C–X · 2373 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 4JK1 · X-ray crystal structure of Escherichia coli sigma70 holoenzyme in complex with Guanosine… · the same entry in another collection · chain Y against Y, TM-score 1.00
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 H0QDQ9
- Every structure of UniProt P00579
- Elsewhere: RCSB PDB 4JK1 · PDBe 4JK1 · UniProt P0A7Z4 · UniProt P0A8V2 · UniProt P0A8T7 · UniProt H0QDQ9 · UniProt P00579
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