MolNFT v1 · #143194 · protein
Crystal structure of thermus thermophilus RNA polymerase core enzyme
6ASG · DNA-directed RNA polymerase subunit beta: “Crystal structure of thermus thermophilus RNA polymerase core enzyme”. X-ray diffraction, 2 ligands (ZN, MG), 20 pockets (best druggability 0.87). MolNFT v1 #143194 on GenesisL1: 3D…
- PDB
- 6ASG
- Type
- protein
- Length
- 2,983 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase subunit beta; DNA-directed RNA polymerase subunit beta'…
- EC
- 2.7.7.6
- UniProt
- Q8RQE9, Q8RQE8, Q5SHR6, Q8RQE7
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 5 distinct chains · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1086 | 28% helix, 24% strand | Q8RQE9 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1356 | 38% helix, 18% strand | Q8RQE8 |
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 226 | 21% helix, 39% strand | Q5SHR6 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 222 | 22% helix, 39% strand | Q5SHR6 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 93 | 49% helix, 10% strand | Q8RQE7 |
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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1092 | 0.87 | 0.88 | 115 | empty |
| 2 | 973 | 0.86 | 0.87 | 107 | empty |
| 3 | 1046 | 0.72 | 0.76 | 89 | empty |
| 4 | 703 | 0.71 | 0.78 | 51 | empty |
| 5 | 168 | 0.69 | 0.89 | 33 | empty |
Interfaces
9 interfaces between chains.
- C–D · 8691 Ų buried · 136 hydrogen bonds · protein-protein
- D–E · 2392 Ų buried · 40 hydrogen bonds · protein-protein
- C–A · 2325 Ų buried · 44 hydrogen bonds · protein-protein
- D–B · 1646 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1639 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6ASG · Crystal structure of Thermus thermophilus RNA polymerase core enzyme · the same entry in another collection · chain C against C, TM-score 1.00
- Q8RQE7 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit omega (Q8RQE7) · a predicted model of the same protein · chain E against A, TM-score 0.97
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 Q8RQE9
- Every structure of UniProt Q8RQE8
- Every structure of UniProt Q5SHR6
- Every structure of UniProt Q8RQE7
- Elsewhere: RCSB PDB 6ASG · PDBe 6ASG · UniProt Q8RQE9 · UniProt Q8RQE8 · UniProt Q5SHR6 · UniProt Q8RQE7
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