Research workbench
Crystal structure of thermus thermophilus RNA polymerase holoenzyme at 3.3 ångströms resolution
Analyse Crystal structure of thermus thermophilus RNA polymerase holoenzyme at 3.3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2CW0
- 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 0.88
Structure
x-ray diffraction · 5 distinct chains · 31% helix, 13% 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 | 14% helix, 24% strand | Q5SHR6 |
| C, M | DNA-directed RNA polymerase beta chain (EC 2.7.7.6) | protein | 1119 | 22% helix, 18% strand | Q8RQE9 |
| D, N | DNA-directed RNA polymerase beta' chain (EC 2.7.7.6) | protein | 1392 | 33% helix, 11% strand | Q8RQE8 |
| E, O | RNA polymerase omega chain (EC 2.7.7.6) | protein | 95 | 44% helix, 4% strand | Q8RQE7 |
| F, P | RNA polymerase sigma factor rpod (EC 2.7.7.6) | protein | 345 | 62% 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 | 1190 | 0.88 | 0.89 | 117 | empty |
| 2 | 994 | 0.87 | 0.88 | 104 | empty |
| 3 | 1166 | 0.86 | 0.87 | 96 | empty |
| 4 | 1124 | 0.84 | 0.85 | 125 | empty |
| 5 | 845 | 0.84 | 0.86 | 81 | empty |
Interfaces
20 interfaces between chains.
- C–D · 9135 Ų buried · 117 hydrogen bonds · protein-protein
- M–N · 8855 Ų buried · 103 hydrogen bonds · protein-protein
- N–P · 4323 Ų buried · 52 hydrogen bonds · protein-protein
- D–F · 4319 Ų buried · 61 hydrogen bonds · protein-protein
- N–O · 2443 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 2CW0 · Crystal structure of Thermus thermophilus RNA polymerase holoenzyme at 3.3 angstroms… · 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 2CW0 · PDBe 2CW0 · UniProt Q5SHR6 · UniProt Q8RQE9 · UniProt Q8RQE8 · UniProt Q8RQE7 · UniProt Q5SKW1
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