Research workbench
Mycobacterium tuberculosis RNAP elongation complex with NusG transcription factor
Analyse Mycobacterium tuberculosis RNAP elongation complex with NusG transcription… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8E82
- Type
- protein + DNA + RNA
- Length
- 3,099 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.03
- Source
- Mycobacterium tuberculosis; SYNTHETIC CONSTRUCT
- Molecule
- DNA-directed RNA polymerase subunit alpha; DNA-directed RNA polymerase subunit beta…
- EC
- 2.7.7.6
- UniProt
- A5U8D3, A5U052, A0A045J9E2, A0A0T9N9K3, A0A045HU92
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · resolution 3.03 · 9 distinct chains · 33% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 226 | 19% helix, 35% strand | A5U8D3 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 237 | 20% helix, 32% strand | A5U8D3 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1095 | 24% helix, 22% strand | A5U052 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1269 | 44% helix, 13% strand | A0A045J9E2 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 82 | 52% helix, 2% strand | A0A0T9N9K3 |
| Z | Transcription termination/antitermination protein NusG | protein | 122 | 33% helix, 29% strand | A0A045HU92 |
| P | DNA (54-mer) | dna | 33 | — | — |
| Q | DNA (54-mer) | dna | 25 | — | — |
| R | RNA (5'-R(P*CP*GP*GP*AP*GP*AP*GP*GP*UP*A)-3') | rna | 10 | — | — |
Ligands and binding sites
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 | 1144 | 0.83 | 0.84 | 112 | empty |
| 2 | 649 | 0.82 | 0.87 | 77 | empty |
| 3 | 705 | 0.82 | 0.86 | 96 | empty |
| 4 | 411 | 0.79 | 0.89 | 53 | empty |
| 5 | 647 | 0.77 | 0.83 | 68 | empty |
Interfaces
20 interfaces between chains.
- C–D · 8108 Ų buried · 89 hydrogen bonds · protein-protein
- A–B · 2454 Ų buried · 9 hydrogen bonds · protein-protein
- D–E · 2261 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 2088 Ų buried · 32 hydrogen bonds · protein-protein
- B–D · 1252 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- A5U052 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta (A5U052) · a predicted model of the same protein · chain C against A, TM-score 0.99
- A5U8D3 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit alpha (A5U8D3) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 A5U8D3
- Every structure of UniProt A5U052
- Every structure of UniProt A0A045J9E2
- Every structure of UniProt A0A0T9N9K3
- Every structure of UniProt A0A045HU92
- Elsewhere: RCSB PDB 8E82 · PDBe 8E82 · UniProt A5U8D3 · UniProt A5U052 · UniProt A0A045J9E2 · UniProt A0A0T9N9K3 · UniProt A0A045HU92
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