Research workbench
Cryoem structure of E.COLI RNA polymerase elongation complex bound to nusa (nusa elongation complex in less-swiveled conformation)
Analyse Cryoem structure of E.COLI RNA polymerase elongation complex bound to nusa… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7PYJ
- Type
- protein + DNA + RNA
- Length
- 3,855 residues
- Chains
- 9
- 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, P0A8V4, P0A8T8, P0A800, D7Y526
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 9 distinct chains · 35% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 229 | 21% helix, 29% strand | P0A7Z4 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 298 | 24% helix, 19% strand | P0A7Z4 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1341 | 31% helix, 22% strand | P0A8V4 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1334 | 38% helix, 16% strand | P0A8T8 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 90 | 69% helix, 0% strand | P0A800 |
| N | Ntdna | dna | 27 | — | — |
| R | RNA | rna | 11 | — | — |
| T | Tdna | dna | 30 | — | — |
| F | Transcription TERMINATION/ANTITERMINATION protein nusa | protein | 495 | 43% helix, 17% strand | D7Y526 |
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 | 1187 | 0.85 | 0.86 | 129 | empty |
| 2 | 404 | 0.82 | 0.91 | 63 | empty |
| 3 | 417 | 0.81 | 0.89 | 61 | empty |
| 4 | 158 | 0.80 | 0.96 | 39 | empty |
| 5 | 110 | 0.79 | 0.97 | 27 | empty |
Interfaces
18 interfaces between chains.
- C–D · 7619 Ų buried · 82 hydrogen bonds · protein-protein
- A–B · 1902 Ų buried · 26 hydrogen bonds · protein-protein
- A–C · 1697 Ų buried · 12 hydrogen bonds · protein-protein
- D–E · 1208 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 929 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7PYJ · CryoEM structure of E.coli RNA polymerase elongation complex bound to NusA (NusA… · the same entry in another collection · chain F against F, TM-score 1.00
- P0A8T8 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta' (P0A8T8) · a predicted model of the same protein · chain D against A, TM-score 0.92
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 P0A8V4
- Every structure of UniProt P0A8T8
- Every structure of UniProt P0A800
- Every structure of UniProt D7Y526
- Elsewhere: RCSB PDB 7PYJ · PDBe 7PYJ · UniProt P0A7Z4 · UniProt P0A8V4 · UniProt P0A8T8 · UniProt P0A800 · UniProt D7Y526
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