MolNFT v2 · #136634 · protein
Escherichia coli RNA polymerase and Rifampin complex, wild-type
5UAC · DNA-directed RNA polymerase subunit alpha: “Escherichia coli RNA polymerase and Rifampin complex, wild-type”. X-ray diffraction at 3.8, 3 ligands (RFP, ZN, MG), 20 pockets (best druggability 0.84). MolNFT v2 #136634 on GenesisL1: 3D…
- PDB
- 5UAC
- Type
- protein
- Length
- 6,988 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.8
- Source
- Escherichia coli (strain K12)
- Molecule
- DNA-directed RNA polymerase subunit alpha; DNA-directed RNA polymerase subunit beta…
- EC
- 2.7.7.6
- UniProt
- P0A7Z4, P0A8V2, P0A8T7, P0A800, P00579
- Ligands
- RFP, ZN, MG
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · resolution 3.8 · 12 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 227 | 21% helix, 34% strand | P0A7Z4 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 214 | 20% helix, 34% strand | P0A7Z4 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1342 | 31% helix, 23% strand | P0A8V2 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1166 | 43% helix, 14% strand | P0A8T7 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 89 | 66% helix, 0% strand | P0A800 |
| F | RNA polymerase sigma factor RpoD | protein | 468 | 69% helix, 3% strand | P00579 |
| G | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 224 | 20% helix, 33% strand | P0A7Z4 |
| H | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 215 | 19% helix, 34% strand | P0A7Z4 |
| I | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1340 | 31% helix, 23% strand | P0A8V2 |
| J | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1155 | 43% helix, 14% strand | P0A8T7 |
| K | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 79 | 63% helix, 0% strand | P0A800 |
| L | RNA polymerase sigma factor RpoD | protein | 469 | 66% helix, 3% strand | P00579 |
Ligands and binding sites
- RFP · Rifampicin · ligand · chains C
- ZN · Zinc ion · metal · 4 copies · chains D, J
- MG · Magnesium ion · metal · 2 copies · chains D, J
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 | 873 | 0.84 | 0.86 | 82 | empty |
| 2 | 574 | 0.82 | 0.87 | 80 | empty |
| 3 | 420 | 0.80 | 0.88 | 46 | empty |
| 4 | 134 | 0.79 | 0.96 | 31 | empty |
| 5 | 674 | 0.77 | 0.82 | 83 | empty |
Interfaces
19 interfaces between chains.
- C–D · 8249 Ų buried · 94 hydrogen bonds · protein-protein
- I–J · 8132 Ų buried · 97 hydrogen bonds · protein-protein
- J–L · 2782 Ų buried · 24 hydrogen bonds · protein-protein
- D–F · 2732 Ų buried · 22 hydrogen bonds · protein-protein
- I–L · 1910 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5UAC · Escherichia COLI RNA polymerase and rifampin complex, wild-type · the same entry in another collection · chain L against L, 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 P0A800
- Every structure of UniProt P00579
- Elsewhere: RCSB PDB 5UAC · PDBe 5UAC · UniProt P0A7Z4 · UniProt P0A8V2 · UniProt P0A8T7 · UniProt P0A800 · UniProt P00579
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