MolNFT v1 · #13391 · protein + DNA
Thermus aquaticus RNA polymerase HOLOENZYME/FORK-junction promoter DNA complex at 6.5 a resolution
1L9Z · Nontemplate DNA strand: “Thermus aquaticus RNA polymerase HOLOENZYME/FORK-junction promoter DNA complex at 6.5 a resolution”. X-ray diffraction, 2 ligands (ZN, MG), 20 pockets (best druggability 0.68). MolNFT v1 #13391 on GenesisL1…
- PDB
- 1L9Z
- Type
- protein + DNA
- Length
- 3,187 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nontemplate DNA strand; Template DNA strand; RNA polymerase, alpha subunit; RNA…
- EC
- 2.7.7.6
- UniProt
- Q9KWU8, Q9KWU7, Q9KWU6, Q9EVV4, Q9EZJ8
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.68
Structure
x-ray diffraction · 8 distinct chains · 0% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| U | Nontemplate DNA strand | dna | 35 | — | — |
| T | Template DNA strand | dna | 30 | — | — |
| A | RNA polymerase, alpha subunit (EC 2.7.7.6) | protein | 224 | 0% helix, 0% strand | Q9KWU8 |
| B | RNA polymerase, alpha subunit (EC 2.7.7.6) | protein | 220 | 0% helix, 0% strand | Q9KWU8 |
| C | RNA polymerase, beta subunit (EC 2.7.7.6) | protein | 1084 | 0% helix, 0% strand | Q9KWU7 |
| D | RNA polymerase, beta-prime subunit (EC 2.7.7.6) | protein | 1183 | 0% helix, 0% strand | Q9KWU6 |
| E | RNA polymerase, omega subunit (EC 2.7.7.6) | protein | 92 | 0% helix, 0% strand | Q9EVV4 |
| H | Sigma factor siga | protein | 319 | 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1167 | 0.68 | 0.73 | 172 | empty |
| 2 | 777 | 0.64 | 0.73 | 108 | ZN |
| 3 | 439 | 0.62 | 0.76 | 86 | empty |
| 4 | 299 | 0.61 | 0.79 | 70 | empty |
| 5 | 520 | 0.59 | 0.73 | 88 | empty |
Interfaces
10 interfaces between chains.
- C–D · 1348 Ų buried · 0 hydrogen bonds · protein-protein
- D–E · 320 Ų buried · 0 hydrogen bonds · protein-protein
- C–H · 291 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 208 Ų buried · 0 hydrogen bonds · protein-protein
- D–H · 181 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 1L9Z · Thermus aquaticus RNA Polymerase Holoenzyme/Fork-Junction Promoter DNA Complex at 6.5 A… · the same entry in another collection · chain H against H, 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 A 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
- Every structure of UniProt Q9EVV4
- Every structure of UniProt Q9EZJ8
- Elsewhere: RCSB PDB 1L9Z · PDBe 1L9Z · UniProt Q9KWU8 · UniProt Q9KWU7 · UniProt Q9KWU6 · UniProt Q9EVV4 · UniProt Q9EZJ8
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