Research workbench
Cryo-EM structure of rifamycin bound to E. COLI rnap and RRNBP1 promoter complex
Analyse Cryo-EM structure of rifamycin bound to E. COLI rnap and RRNBP1 promoter complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7SZJ
- Type
- protein + DNA
- Length
- 3,789 residues
- Chains
- 8
- 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
- Ligands
- RFP, ZN, MG
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 8 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 | 231 | 23% helix, 36% strand | P0A7Z4 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 230 | 23% helix, 38% strand | P0A7Z4 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1340 | 32% helix, 21% strand | P0A8V2 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1340 | 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 | 466 | 70% helix, 3% strand | P00579 |
| X | DNA (57-mer) | dna | 57 | — | — |
| Y | DNA (49-mer) | dna | 49 | — | — |
Ligands and binding sites
- RFP · Rifampicin · ligand · chains C
- ZN · Zinc ion · metal · 2 copies · chains D
- MG · Magnesium ion · metal · 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 | 794 | 0.81 | 0.84 | 66 | empty |
| 2 | 829 | 0.78 | 0.82 | 89 | empty |
| 3 | 1063 | 0.78 | 0.80 | 76 | empty |
| 4 | 965 | 0.77 | 0.79 | 99 | empty |
| 5 | 1129 | 0.77 | 0.79 | 111 | empty |
Interfaces
16 interfaces between chains.
- C–D · 8161 Ų buried · 76 hydrogen bonds · protein-protein
- D–F · 2404 Ų buried · 18 hydrogen bonds · protein-protein
- X–Y · 2173 Ų buried · 209 hydrogen bonds · nucleic-nucleic
- A–B · 2118 Ų buried · 7 hydrogen bonds · protein-protein
- C–F · 1932 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 7SZJ · Cryo-EM structure of Rifamycin bound to E. coli RNAP and rrnBP1 promoter complex · the same entry in another collection · chain A against A, 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 7SZJ · PDBe 7SZJ · UniProt P0A7Z4 · UniProt P0A8V2 · UniProt P0A8T7 · UniProt P0A800 · UniProt P00579
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