Research workbench
Recombinant thermus aquaticus RNA polymerase for structural studies
Analyse Recombinant thermus aquaticus RNA polymerase for structural studies in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GHO
- Type
- protein
- Length
- 2,765 residues
- Chains
- 4
- 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
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 25% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 230 | 19% helix, 18% strand | Q9KWU8 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 225 | 16% helix, 28% strand | Q9KWU8 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1114 | 17% helix, 13% strand | Q9KWU7 |
| D | DNA-directed RNA polymerase subunit BETA',DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1196 | 36% helix, 8% strand | Q9KWU6 |
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 692 | 0.73 | 0.80 | 91 | empty |
| 2 | 856 | 0.70 | 0.77 | 121 | empty |
| 3 | 858 | 0.70 | 0.77 | 104 | empty |
| 4 | 1103 | 0.70 | 0.75 | 92 | empty |
| 5 | 528 | 0.69 | 0.80 | 94 | empty |
Interfaces
5 interfaces between chains.
- C–D · 1818 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 303 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 206 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 86 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 24 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2GHO · Recombinant Thermus aquaticus RNA polymerase for Structural Studies · the same entry in another collection · chain D against D, 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 0.96
- 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 0.95
- Q9KWU8 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit alpha (Q9KWU8) · a predicted model of the same protein · chain B 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 Q9KWU8
- Every structure of UniProt Q9KWU7
- Every structure of UniProt Q9KWU6
- Elsewhere: RCSB PDB 2GHO · PDBe 2GHO · UniProt Q9KWU8 · UniProt Q9KWU7 · UniProt Q9KWU6
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