Research workbench
Cryo-EM structure of HK022 putrna-associated E.COLI RNA polymerase elongation complex
Analyse Cryo-EM structure of HK022 putrna-associated E.COLI RNA polymerase elongation… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7XUE
- Type
- protein + DNA + RNA
- Length
- 3,335 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non-template DNA; Template DNA; RNA (nun gene and immunity region); DNA-directed RNA…
- EC
- 2.7.7.6
- UniProt
- P0A7Z4, P0A8V2, P0A8T7, P0A800
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 8 distinct chains · 32% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Non-template DNA | dna | 21 | — | — |
| B | Template DNA | dna | 30 | — | — |
| R | RNA (nun gene and immunity region) | rna | 85 | — | — |
| G | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 221 | 22% helix, 36% strand | P0A7Z4 |
| H | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 219 | 19% helix, 35% strand | P0A7Z4 |
| I | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1341 | 30% helix, 22% strand | P0A8V2 |
| J | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1335 | 36% helix, 18% strand | P0A8T7 |
| K | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 83 | 66% helix, 0% strand | P0A800 |
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 | 842 | 0.84 | 0.86 | 86 | empty |
| 2 | 1007 | 0.84 | 0.85 | 84 | empty |
| 3 | 840 | 0.82 | 0.84 | 77 | empty |
| 4 | 842 | 0.82 | 0.85 | 74 | empty |
| 5 | 661 | 0.78 | 0.83 | 52 | empty |
Interfaces
15 interfaces between chains.
- I–J · 8170 Ų buried · 81 hydrogen bonds · protein-protein
- G–H · 1893 Ų buried · 6 hydrogen bonds · protein-protein
- G–I · 1697 Ų buried · 14 hydrogen bonds · protein-protein
- R–J · 1588 Ų buried · 25 hydrogen bonds · protein-nucleic
- J–K · 1253 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 7XUE · Cryo-EM structure of HK022 putRNA-associated E.coli RNA polymerase elongation complex · the same entry in another collection · chain A against A, TM-score 1.00
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 7XUE · PDBe 7XUE · UniProt P0A7Z4 · UniProt P0A8V2 · UniProt P0A8T7 · UniProt P0A800
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