Research workbench
Crystal structure of thermus aquaticus core RNA polymerase-includes complete structure with side-chains (except for disordered regions)- further refined from original deposition-contains additional sequence information
Analyse Crystal structure of thermus aquaticus core RNA polymerase-includes complete… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1HQM
- Type
- protein
- Length
- 2,838 residues
- Chains
- 5
- 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
- Q9KWU8, Q9KWU7, Q9KWU6, Q9EVV4
- Ligands
- MG, ZN
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 25% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 223 | 19% helix, 15% strand | Q9KWU8 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 229 | 16% helix, 15% strand | Q9KWU8 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1113 | 20% helix, 11% strand | Q9KWU7 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1175 | 30% helix, 5% strand | Q9KWU6 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 98 | 38% helix, 2% strand | Q9EVV4 |
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 | 718 | 0.83 | 0.86 | 73 | empty |
| 2 | 216 | 0.81 | 0.94 | 50 | empty |
| 3 | 98 | 0.77 | 0.97 | 34 | empty |
| 4 | 173 | 0.76 | 0.92 | 35 | empty |
| 5 | 539 | 0.76 | 0.83 | 82 | empty |
Interfaces
8 interfaces between chains.
- C–D · 7809 Ų buried · 101 hydrogen bonds · protein-protein
- A–C · 2115 Ų buried · 43 hydrogen bonds · protein-protein
- D–E · 2071 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1763 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 1020 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 1HQM · Crystal structure of thermus aquaticus core RNA polymerase-includes complete structure… · the same entry in another collection · chain E against E, TM-score 1.00
- Q9KWU7 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta (Q9KWU7) · a predicted model of the same protein · chain C against A, TM-score 0.94
- Q9KWU8 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit alpha (Q9KWU8) · a predicted model of the same protein · chain A against A, TM-score 0.93
- Q9KWU6 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta' (Q9KWU6) · a predicted model of the same protein · chain D against A, TM-score 0.92
- Q9EVV4 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit omega (Q9EVV4) · a predicted model of the same protein · chain E against A, TM-score 0.87
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 Q9KWU8
- Every structure of UniProt Q9KWU7
- Every structure of UniProt Q9KWU6
- Every structure of UniProt Q9EVV4
- Elsewhere: RCSB PDB 1HQM · PDBe 1HQM · UniProt Q9KWU8 · UniProt Q9KWU7 · UniProt Q9KWU6 · UniProt Q9EVV4
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