MolNFT v1 · #148950 · protein + DNA + RNA
Cryoem structure of E.COLI RNA polymerase paused elongation complex without RNA hairpin bound to nusa
6FLP · DNA-directed RNA polymerase subunit alpha: “Cryoem structure of E.COLI RNA polymerase paused elongation complex without RNA hairpin bound to nusa”. Electron microscopy, 2 ligands (ZN, MG), 20 pockets (best druggability 0.83). MolNFT…
- PDB
- 6FLP
- Type
- protein + DNA + RNA
- Length
- 3,264 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
- P0A7Z4, P0A8V2, P0A8T7, P0A800
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 8 distinct chains · 32% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 229 | 22% helix, 31% strand | P0A7Z4 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 217 | 19% helix, 27% strand | P0A7Z4 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1314 | 30% helix, 19% strand | P0A8V2 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1334 | 35% helix, 14% strand | P0A8T7 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 90 | 68% helix, 0% strand | P0A800 |
| N | DNA (30-mer) | dna | 31 | — | — |
| R | RNA (5'-R(P*GP*AP*UP*GP*UP*GP*UP*GP*CP*U)-3') | rna | 10 | — | — |
| T | DNA (39-mer) | dna | 39 | — | — |
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 | 989 | 0.83 | 0.85 | 86 | empty |
| 2 | 843 | 0.83 | 0.85 | 78 | empty |
| 3 | 500 | 0.81 | 0.88 | 62 | empty |
| 4 | 553 | 0.81 | 0.87 | 65 | empty |
| 5 | 688 | 0.79 | 0.84 | 70 | empty |
Interfaces
15 interfaces between chains.
- C–D · 8212 Ų buried · 72 hydrogen bonds · protein-protein
- A–C · 1817 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1661 Ų buried · 6 hydrogen bonds · protein-protein
- N–T · 1336 Ų buried · 97 hydrogen bonds · nucleic-nucleic
- D–E · 1201 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6FLP · CryoEM structure of E.coli RNA polymerase paused elongation complex without RNA hairpin… · the same entry in another collection · chain T against T, 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 0.97
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 P0A7Z4
- Every structure of UniProt P0A8V2
- Every structure of UniProt P0A8T7
- Every structure of UniProt P0A800
- Elsewhere: RCSB PDB 6FLP · PDBe 6FLP · UniProt P0A7Z4 · UniProt P0A8V2 · UniProt P0A8T7 · UniProt P0A800
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