MolNFT v1 · #9771 · protein
Thermus aquaticus core RNA polymerase-rifampicin complex
1I6V · DNA-directed RNA polymerase: “Thermus aquaticus core RNA polymerase-rifampicin complex”. X-ray diffraction, 3 ligands (RFP, MG, ZN), 20 pockets (best druggability 0.85). MolNFT v1 #9771 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1I6V
- Type
- protein
- Length
- 2,839 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase
- EC
- 2.7.7.6
- UniProt
- Q9KWU8, Q9KWU7, Q9KWU6, Q9EVV4
- Ligands
- RFP, MG, ZN
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 24% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase (EC 2.7.7.6) | protein | 224 | 18% helix, 18% strand | Q9KWU8 |
| B | DNA-directed RNA polymerase (EC 2.7.7.6) | protein | 230 | 15% helix, 15% strand | Q9KWU8 |
| C | DNA-directed RNA polymerase (EC 2.7.7.6) | protein | 1113 | 19% helix, 11% strand | Q9KWU7 |
| D | DNA-directed RNA polymerase (EC 2.7.7.6) | protein | 1174 | 31% helix, 6% strand | Q9KWU6 |
| E | DNA-directed RNA polymerase (EC 2.7.7.6) | protein | 98 | 35% helix, 2% strand | Q9EVV4 |
Ligands and binding sites
- RFP · Rifampicin · ligand · chains C
- MG · Magnesium ion · metal · chains D
- ZN · Zinc ion · metal · chains D
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 | 950 | 0.85 | 0.87 | 90 | empty |
| 2 | 172 | 0.78 | 0.94 | 46 | empty |
| 3 | 707 | 0.77 | 0.82 | 65 | empty |
| 4 | 293 | 0.75 | 0.88 | 40 | empty |
| 5 | 841 | 0.75 | 0.79 | 74 | empty |
Interfaces
8 interfaces between chains.
- C–D · 7961 Ų buried · 107 hydrogen bonds · protein-protein
- A–C · 2205 Ų buried · 40 hydrogen bonds · protein-protein
- D–E · 2101 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1795 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 1063 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 1I6V · Thermus aquaticus core RNA polymerase-rifampicin complex · the same entry in another collection · chain E against E, 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 0.94
- 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
- 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 0.92
- Q9EVV4 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit omega (Q9EVV4) · a predicted model of the same protein · chain E against A, TM-score 0.86
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
- Elsewhere: RCSB PDB 1I6V · PDBe 1I6V · UniProt Q9KWU8 · UniProt Q9KWU7 · UniProt Q9KWU6 · UniProt Q9EVV4
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