Research workbench
Cryoem structure of E.COLI RNA polymerase paused elongation complex without RNA hairpin bound to nusa
Analyse Cryoem structure of E.COLI RNA polymerase paused elongation complex without RNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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