Research workbench
Cuer-tac without RNA
Analyse Cuer-tac without RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XH7
- Type
- protein + DNA
- Length
- 4,073 residues
- Chains
- 10
- 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
- P0A7Z6, B7MIX3, P0A8T8, B7MFL0, P00579, P0A9G4
- Ligands
- ZN, CU
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 9 distinct chains · 37% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 230 | 22% helix, 30% strand | P0A7Z6 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 228 | 21% helix, 34% strand | P0A7Z6 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1340 | 29% helix, 21% strand | B7MIX3 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1337 | 35% helix, 15% strand | P0A8T8 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 79 | 62% helix, 0% strand | B7MFL0 |
| F | RNA polymerase sigma factor rpod | protein | 497 | 65% helix, 0% strand | P00579 |
| G, H | Hth-type transcriptional regulator cuer | protein | 130 | 66% helix, 2% strand | P0A9G4 |
| 1 | Nontemplate strand DNA (54-mer) | dna | 54 | — | — |
| 2 | Template strand DNA (54-mer) | dna | 48 | — | — |
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 | 1048 | 0.84 | 0.85 | 99 | empty |
| 2 | 1034 | 0.84 | 0.85 | 124 | empty |
| 3 | 1139 | 0.84 | 0.85 | 147 | empty |
| 4 | 216 | 0.82 | 0.94 | 43 | empty |
| 5 | 242 | 0.80 | 0.92 | 58 | empty |
Interfaces
22 interfaces between chains.
- C–D · 7704 Ų buried · 68 hydrogen bonds · protein-protein
- D–F · 2395 Ų buried · 23 hydrogen bonds · protein-protein
- G–H · 2242 Ų buried · 25 hydrogen bonds · protein-protein
- C–F · 2051 Ų buried · 15 hydrogen bonds · protein-protein
- 1–2 · 1855 Ų buried · 182 hydrogen bonds · nucleic-nucleic
Compared structures
- 6XH7 · CueR-TAC without RNA · the same entry in another collection · chain 2 against 2, TM-score 1.00
- B7MIX3 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit beta (B7MIX3) · a predicted model of the same protein · chain C against A, TM-score 0.97
- P0A9G4 · AlphaFold monomer V2.0 prediction for hth-type transcriptional regulator cuer (P0A9G4) · a predicted model of the same protein · chain H against A, TM-score 0.94
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 P0A7Z6
- Every structure of UniProt B7MIX3
- Every structure of UniProt P0A8T8
- Every structure of UniProt B7MFL0
- Every structure of UniProt P00579
- Every structure of UniProt P0A9G4
- Elsewhere: RCSB PDB 6XH7 · PDBe 6XH7 · UniProt P0A7Z6 · UniProt B7MIX3 · UniProt P0A8T8 · UniProt B7MFL0 · UniProt P00579 · UniProt P0A9G4
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