MolNFT v1 · #162714 · protein + DNA + RNA
Cryo-EM structure of E. COLI RNA polymerase elongation complex bound to CTP substrate
6RH3 · Non-template DNA: “Cryo-EM structure of E. COLI RNA polymerase elongation complex bound to CTP substrate”. Electron microscopy, 3 ligands (CTP, ZN, MG), 20 pockets (best druggability 0.84). MolNFT v1 #162714 on GenesisL1: 3D…
- PDB
- 6RH3
- Type
- protein + DNA + RNA
- Length
- 3,265 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non-template DNA; Template DNA; DNA-directed RNA polymerase subunit alpha; DNA-directed…
- EC
- 2.7.7.6
- UniProt
- P0A7Z4, P0A8V2, P0A8T7, L4IY67
- Ligands
- CTP, ZN, MG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 8 distinct chains · 32% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| N | Non-template DNA | dna | 19 | — | — |
| T | Template DNA | dna | 29 | — | — |
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 228 | 19% helix, 36% strand | P0A7Z4 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 229 | 19% helix, 34% strand | P0A7Z4 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1319 | 29% helix, 20% strand | P0A8V2 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1358 | 37% helix, 17% strand | P0A8T7 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 73 | 59% helix, 0% strand | L4IY67 |
| R | RNA | rna | 10 | — | — |
Ligands and binding sites
- CTP · Cytidine-5'-triphosphate · ligand · chains T, C, D, R
- ZN · Zinc ion · metal · 2 copies · chains D
- MG · Magnesium 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 | 1030 | 0.84 | 0.85 | 96 | empty |
| 2 | 652 | 0.83 | 0.88 | 65 | CTP, MG |
| 3 | 425 | 0.80 | 0.89 | 43 | empty |
| 4 | 902 | 0.80 | 0.82 | 82 | empty |
| 5 | 438 | 0.78 | 0.87 | 51 | empty |
Interfaces
15 interfaces between chains.
- C–D · 8452 Ų buried · 86 hydrogen bonds · protein-protein
- A–B · 2000 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 1913 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 1267 Ų buried · 8 hydrogen bonds · protein-protein
- T–D · 1001 Ų buried · 10 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 6RH3 · Cryo-EM structure of E. coli RNA polymerase elongation complex bound to CTP substrate · the same entry in another collection · chain R against R, TM-score 1.00
- P0A8V2 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta (P0A8V2) · a predicted model of the same protein · chain C against A, TM-score 0.99
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 P0A7Z4
- Every structure of UniProt P0A8V2
- Every structure of UniProt P0A8T7
- Every structure of UniProt L4IY67
- Elsewhere: RCSB PDB 6RH3 · PDBe 6RH3 · UniProt P0A7Z4 · UniProt P0A8V2 · UniProt P0A8T7 · UniProt L4IY67
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