Research workbench
E. COLI RNA polymerase complexed with nusg
Analyse E. COLI RNA polymerase complexed with nusg in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TBZ
- Type
- protein
- Length
- 6,421 residues
- Chains
- 10
- Method
- x-ray diffraction
- 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
- P0A7Z6, B7MIX3, P0A8T8, P0AFG1
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 7 distinct chains · 28% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 225 | 19% helix, 26% strand | P0A7Z6 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 215 | 17% helix, 27% strand | P0A7Z6 |
| C, H | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1319 | 28% helix, 17% strand | B7MIX3 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1302 | 31% helix, 10% strand | P0A8T8 |
| G | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 216 | 17% helix, 26% strand | P0A7Z6 |
| I | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1306 | 30% helix, 10% strand | P0A8T8 |
| J, K | Transcription TERMINATION/ANTITERMINATION protein nusg | protein | 147 | 23% helix, 29% strand | P0AFG1 |
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 | 1103 | 0.83 | 0.84 | 136 | empty |
| 2 | 956 | 0.82 | 0.83 | 98 | empty |
| 3 | 992 | 0.82 | 0.83 | 80 | empty |
| 4 | 512 | 0.82 | 0.88 | 66 | empty |
| 5 | 308 | 0.81 | 0.91 | 58 | empty |
Interfaces
22 interfaces between chains.
- H–I · 8275 Ų buried · 96 hydrogen bonds · protein-protein
- C–D · 8223 Ų buried · 95 hydrogen bonds · protein-protein
- D–I · 2435 Ų buried · 28 hydrogen bonds · protein-protein
- F–G · 1830 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1797 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- B7MIX3 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta (B7MIX3) · a predicted model of the same protein · chain C against A, TM-score 0.96
- P0A7Z6 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit alpha (P0A7Z6) · a predicted model of the same protein · chain G against A, TM-score 0.94
- P0A8T8 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta' (P0A8T8) · a predicted model of the same protein · chain I against A, TM-score 0.88
- P0AFG1 · AlphaFold monomer V2.0 prediction for transcription TERMINATION/ANTITERMINATION protein… · a predicted model of the same protein · chain J against A, TM-score 0.45
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 P0A7Z6
- Every structure of UniProt B7MIX3
- Every structure of UniProt P0A8T8
- Every structure of UniProt P0AFG1
- Elsewhere: RCSB PDB 5TBZ · PDBe 5TBZ · UniProt P0A7Z6 · UniProt B7MIX3 · UniProt P0A8T8 · UniProt P0AFG1
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