MolNFT v1 · #156504 · protein + DNA + RNA
Cryoem structure of thermus thermophilus RNA polymerase elongation complex
6M6C · DNA-directed RNA polymerase subunit alpha: “Cryoem structure of thermus thermophilus RNA polymerase elongation complex”. Electron microscopy, 2 ligands (ZN, MG), 20 pockets (best druggability 0.85). MolNFT v1 #156504 on GenesisL1…
- PDB
- 6M6C
- Type
- protein + DNA + RNA
- Length
- 3,017 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase subunit alpha; DNA-directed RNA polymerase subunit beta…
- EC
- 2.7.7.6
- UniProt
- Q5SHR6, Q8RQE9, Q8RQE8, Q8RQE7
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 8 distinct chains · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 226 | 21% helix, 38% strand | Q5SHR6 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 222 | 23% helix, 42% strand | Q5SHR6 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1111 | 29% helix, 27% strand | Q8RQE9 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1305 | 41% helix, 19% strand | Q8RQE8 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 94 | 52% helix, 12% strand | Q8RQE7 |
| R | RNA | rna | 10 | — | — |
| N | Nontemplate strand DNA | dna | 20 | — | — |
| T | Template strand DNA | dna | 29 | — | — |
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 | 941 | 0.85 | 0.86 | 96 | empty |
| 2 | 461 | 0.81 | 0.89 | 57 | empty |
| 3 | 832 | 0.81 | 0.84 | 81 | empty |
| 4 | 702 | 0.79 | 0.84 | 68 | empty |
| 5 | 513 | 0.78 | 0.85 | 65 | empty |
Interfaces
17 interfaces between chains.
- C–D · 8988 Ų buried · 98 hydrogen bonds · protein-protein
- D–E · 2516 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 2060 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1524 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 1228 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 6M6C · CryoEM structure of Thermus thermophilus RNA polymerase elongation complex · the same entry in another collection · chain T against T, 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 0.98
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
- Elsewhere: RCSB PDB 6M6C · PDBe 6M6C · UniProt Q5SHR6 · UniProt Q8RQE9 · UniProt Q8RQE8 · UniProt Q8RQE7
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