Research workbench
T. thermophilus RNA polymerase holoenzyme bound with GP39 and GP76
Analyse T. thermophilus RNA polymerase holoenzyme bound with GP39 and GP76 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XJ0
- Type
- protein
- Length
- 3,693 residues
- Chains
- 9
- 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
- Q5SHR6, Q8RQE9, Q8RQE8, Q8RQE7, Q5SKW1, A7XX65, A7XXA7
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 9 distinct chains · 32% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 225 | 20% helix, 39% strand | Q5SHR6 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 232 | 20% helix, 41% strand | Q5SHR6 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1114 | 26% helix, 23% strand | Q8RQE9 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1462 | 35% helix, 17% strand | Q8RQE8 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 95 | 46% helix, 4% strand | Q8RQE7 |
| F | RNA polymerase sigma factor siga | protein | 313 | 59% helix, 1% strand | Q5SKW1 |
| G | GP39 | protein | 127 | 14% helix, 35% strand | A7XX65 |
| H | GP39 | protein | 91 | 8% helix, 35% strand | A7XX65 |
| Y | GP76 | protein | 34 | 65% helix, 3% strand | A7XXA7 |
Ligands and binding sites
- ZN · Zinc 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 | 988 | 0.87 | 0.88 | 97 | empty |
| 2 | 1137 | 0.86 | 0.87 | 99 | empty |
| 3 | 465 | 0.82 | 0.89 | 48 | empty |
| 4 | 368 | 0.80 | 0.89 | 61 | empty |
| 5 | 441 | 0.79 | 0.87 | 63 | empty |
Interfaces
20 interfaces between chains.
- C–D · 8466 Ų buried · 103 hydrogen bonds · protein-protein
- D–F · 3572 Ų buried · 40 hydrogen bonds · protein-protein
- D–E · 2510 Ų buried · 38 hydrogen bonds · protein-protein
- A–C · 2210 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1867 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 5XJ0 · T. thermophilus RNA polymerase holoenzyme bound with gp39 and gp76 · the same entry in another collection · chain G against G, TM-score 1.00
- Q8RQE7 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit omega (Q8RQE7) · a predicted model of the same protein · chain E against A, TM-score 0.90
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 Q5SHR6
- Every structure of UniProt Q8RQE9
- Every structure of UniProt Q8RQE8
- Every structure of UniProt Q8RQE7
- Every structure of UniProt Q5SKW1
- Every structure of UniProt A7XX65
- Every structure of UniProt A7XXA7
- Elsewhere: RCSB PDB 5XJ0 · PDBe 5XJ0 · UniProt Q5SHR6 · UniProt Q8RQE9 · UniProt Q8RQE8 · UniProt Q8RQE7 · UniProt Q5SKW1 · UniProt A7XX65 · UniProt A7XXA7
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