Research workbench
Cryo-EM structure of a Q-engaged arrested complex
Analyse Cryo-EM structure of a Q-engaged arrested complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6JNX
- Type
- protein + DNA + RNA
- Length
- 3,915 residues
- Chains
- 11
- 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, P00579, M1FPN0
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 11 distinct chains · 37% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 219 | 20% helix, 32% strand | P0A7Z4 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 218 | 21% helix, 38% strand | P0A7Z4 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1340 | 30% helix, 21% strand | P0A8V2 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1335 | 35% helix, 16% strand | P0A8T7 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 79 | 59% helix, 0% strand | P0A800 |
| F | RNA polymerase sigma factor rpod | protein | 307 | 72% helix, 2% strand | P00579 |
| N | DNA (63-mer) | dna | 63 | — | — |
| R | RNA (5'- R(P*AP*UP*AP*AP*GP*GP*UP*GP*GP*GP*GP*UP*UP*AP*GP*UP*GP*A)-3') | rna | 18 | — | — |
| T | DNA (63-mer) | dna | 63 | — | — |
| P | Antiterminator Q protein | protein | 147 | 62% helix, 0% strand | M1FPN0 |
| Q | Antiterminator Q protein | protein | 126 | 65% helix, 3% strand | M1FPN0 |
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 | 984 | 0.87 | 0.89 | 109 | empty |
| 2 | 838 | 0.83 | 0.86 | 94 | empty |
| 3 | 880 | 0.83 | 0.85 | 86 | empty |
| 4 | 721 | 0.80 | 0.84 | 71 | empty |
| 5 | 584 | 0.77 | 0.84 | 70 | empty |
Interfaces
28 interfaces between chains.
- C–D · 7736 Ų buried · 93 hydrogen bonds · protein-protein
- N–T · 2221 Ų buried · 262 hydrogen bonds · nucleic-nucleic
- A–B · 1753 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 1678 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 1252 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6JNX · Cryo-EM structure of a Q-engaged arrested complex · the same entry in another collection · chain Q against Q, 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
- Every structure of UniProt P00579
- Every structure of UniProt M1FPN0
- Elsewhere: RCSB PDB 6JNX · PDBe 6JNX · UniProt P0A7Z4 · UniProt P0A8V2 · UniProt P0A8T7 · UniProt P0A800 · UniProt P00579 · UniProt M1FPN0
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