Research workbench
Structural basis of transcription inhibition by the DNA mimic ocr protein of bacteriophage T7
Analyse Structural basis of transcription inhibition by the DNA mimic ocr protein of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6R9G
- Type
- protein
- Length
- 3,421 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, P0A800, P03775
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 7 distinct chains · 31% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 230 | 16% helix, 27% strand | P0A7Z4 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 231 | 19% helix, 26% strand | P0A7Z4 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1341 | 28% helix, 15% strand | P0A8V2 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1334 | 33% helix, 7% strand | P0A8T7 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 75 | 57% helix, 0% strand | P0A800 |
| G | Overcome classical restriction GP0.3 | protein | 104 | 66% helix, 0% strand | P03775 |
| F | Overcome classical restriction GP0.3 | protein | 106 | 59% 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 | 1089 | 0.87 | 0.88 | 129 | empty |
| 2 | 1139 | 0.86 | 0.87 | 128 | empty |
| 3 | 867 | 0.86 | 0.88 | 95 | empty |
| 4 | 990 | 0.84 | 0.85 | 110 | empty |
| 5 | 336 | 0.82 | 0.92 | 58 | empty |
Interfaces
13 interfaces between chains.
- C–D · 7387 Ų buried · 54 hydrogen bonds · protein-protein
- A–C · 1947 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 1876 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 1570 Ų buried · 14 hydrogen bonds · protein-protein
- C–F · 1344 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6R9G · Structural basis of transcription inhibition by the DNA mimic Ocr protein of… · the same entry in another collection · chain F against F, 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 0.94
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 P03775
- Elsewhere: RCSB PDB 6R9G · PDBe 6R9G · UniProt P0A7Z4 · UniProt P0A8V2 · UniProt P0A8T7 · UniProt P0A800 · UniProt P03775
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