MolNFT v1 · #162444 · protein
Cryo-EM structure of bacterial rnap with a DNA mimic protein ocr from T7 phage
6R9B · DNA-directed RNA polymerase subunit alpha: “Cryo-EM structure of bacterial rnap with a DNA mimic protein ocr from T7 phage”. Electron microscopy, 20 pockets (best druggability 0.85). MolNFT v1 #162444 on GenesisL1: 3D structure…
- PDB
- 6R9B
- Type
- protein
- Length
- 3,401 residues
- Chains
- 7
- 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, F4NQ47, P03775
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 7 distinct chains · 31% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 233 | 19% helix, 22% strand | P0A7Z4 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 221 | 17% helix, 19% strand | P0A7Z4 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1341 | 28% helix, 14% strand | P0A8V2 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1323 | 32% helix, 6% strand | P0A8T7 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 74 | 62% helix, 0% strand | F4NQ47 |
| F | Overcome classical restriction GP0.3 | protein | 104 | 67% helix, 0% strand | P03775 |
| G | Overcome classical restriction GP0.3 | protein | 105 | 67% helix, 0% strand | P03775 |
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 | 813 | 0.85 | 0.88 | 100 | empty |
| 2 | 785 | 0.80 | 0.83 | 77 | empty |
| 3 | 1077 | 0.80 | 0.81 | 77 | empty |
| 4 | 1024 | 0.80 | 0.81 | 116 | empty |
| 5 | 382 | 0.80 | 0.89 | 58 | empty |
Interfaces
13 interfaces between chains.
- C–D · 7917 Ų buried · 45 hydrogen bonds · protein-protein
- A–B · 1914 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 1741 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 1183 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 1141 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6R9B · Cryo-EM structure of bacterial RNAP with a DNA mimic protein Ocr from T7 phage · the same entry in another collection · chain G against G, TM-score 1.00
- P0A8V2 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta (P0A8V2) · a predicted model of the same protein · chain C against A, TM-score 0.95
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 F4NQ47
- Every structure of UniProt P03775
- Elsewhere: RCSB PDB 6R9B · PDBe 6R9B · UniProt P0A7Z4 · UniProt P0A8V2 · UniProt P0A8T7 · UniProt F4NQ47 · UniProt P03775
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