Research workbench
Thermus aquaticus RNA polymerase holoenzyme at 4 a resolution
Analyse Thermus aquaticus RNA polymerase holoenzyme at 4 a resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1L9U
- Type
- protein
- Length
- 6,250 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA polymerase, alpha subunit; RNA polymerase, beta subunit; RNA polymerase, beta-prime…
- EC
- 2.7.7.6
- UniProt
- Q9KWU8, Q9KWU7, Q9KWU6, Q9EVV4, Q9EZJ8
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.73
Structure
x-ray diffraction · 6 distinct chains · 0% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, J | RNA polymerase, alpha subunit (EC 2.7.7.6) | protein | 224 | 0% helix, 0% strand | Q9KWU8 |
| B, K | RNA polymerase, alpha subunit (EC 2.7.7.6) | protein | 220 | 0% helix, 0% strand | Q9KWU8 |
| C, L | RNA polymerase, beta subunit (EC 2.7.7.6) | protein | 1084 | 0% helix, 0% strand | Q9KWU7 |
| D, M | RNA polymerase, beta-prime subunit (EC 2.7.7.6) | protein | 1183 | 0% helix, 0% strand | Q9KWU6 |
| E, N | RNA polymerase, omega subunit (EC 2.7.7.6) | protein | 92 | 0% helix, 0% strand | Q9EVV4 |
| H, Q | Sigma factor siga | protein | 322 | 0% helix, 0% strand | Q9EZJ8 |
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 | 1058 | 0.73 | 0.76 | 159 | empty |
| 2 | 1136 | 0.68 | 0.73 | 159 | empty |
| 3 | 1060 | 0.68 | 0.73 | 168 | empty |
| 4 | 630 | 0.67 | 0.76 | 114 | empty |
| 5 | 579 | 0.65 | 0.76 | 92 | empty |
Interfaces
18 interfaces between chains.
- L–M · 1305 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 1301 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 296 Ų buried · 0 hydrogen bonds · protein-protein
- J–L · 292 Ų buried · 0 hydrogen bonds · protein-protein
- D–E · 264 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1L9U · Thermus aquaticus RNA polymerase holoenzyme at 4 a resolution · the same entry in another collection · chain H against H, 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 Q9KWU8
- Every structure of UniProt Q9KWU7
- Every structure of UniProt Q9KWU6
- Every structure of UniProt Q9EVV4
- Every structure of UniProt Q9EZJ8
- Elsewhere: RCSB PDB 1L9U · PDBe 1L9U · UniProt Q9KWU8 · UniProt Q9KWU7 · UniProt Q9KWU6 · UniProt Q9EVV4 · UniProt Q9EZJ8
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