Research workbench
Crystal structure of the T. thermophilus RNA polymerase holoenzyme
Analyse Crystal structure of the T. thermophilus RNA polymerase holoenzyme in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2A6E
- Type
- protein
- Length
- 6,818 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase alpha chain; DNA-directed RNA polymerase beta chain…
- EC
- 2.7.7.6
- UniProt
- Q5SHR6, Q8RQE9, Q8RQE8, Q8RQE7, Q5SKW1
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 5 distinct chains · 36% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, K, L | DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) | protein | 229 | 21% helix, 40% strand | Q5SHR6 |
| C, M | DNA-directed RNA polymerase beta chain (EC 2.7.7.6) | protein | 1119 | 26% helix, 21% strand | Q8RQE9 |
| D, N | DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) | protein | 1392 | 39% helix, 13% strand | Q8RQE8 |
| E, O | RNA polymerase omega chain | protein | 95 | 49% helix, 4% strand | Q8RQE7 |
| F, P | RNA polymerase sigma factor rpod | protein | 345 | 67% helix, 1% strand | Q5SKW1 |
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 | 1099 | 0.86 | 0.86 | 108 | empty |
| 2 | 810 | 0.84 | 0.87 | 81 | empty |
| 3 | 523 | 0.84 | 0.90 | 65 | empty |
| 4 | 456 | 0.84 | 0.91 | 65 | empty |
| 5 | 803 | 0.84 | 0.87 | 90 | empty |
Interfaces
19 interfaces between chains.
- C–D · 9276 Ų buried · 125 hydrogen bonds · protein-protein
- M–N · 9044 Ų buried · 118 hydrogen bonds · protein-protein
- N–P · 4128 Ų buried · 53 hydrogen bonds · protein-protein
- D–F · 3953 Ų buried · 65 hydrogen bonds · protein-protein
- N–O · 2458 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 2A6E · Crystal structure of the T. Thermophilus RNA polymerase holoenzyme · the same entry in another collection · chain P against P, TM-score 1.00
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
- Elsewhere: RCSB PDB 2A6E · PDBe 2A6E · UniProt Q5SHR6 · UniProt Q8RQE9 · UniProt Q8RQE8 · UniProt Q8RQE7 · UniProt Q5SKW1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.