MolNFT v1 · #160119 · protein + DNA + RNA
The E. COLI class-II cap-dependent transcription activation complex with de novo RNA transcript at the state 2
6PB4 · DNA-directed RNA polymerase subunit alpha: “The E. COLI class-II cap-dependent transcription activation complex with de novo RNA transcript at the state 2”. Electron microscopy, 3 ligands (CMP, ZN, MG), 20 pockets (best druggability…
- PDB
- 6PB4
- Type
- protein + DNA + RNA
- Length
- 4,250 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
- P0A7Z6, B7MIX3, P0A8T8, B7MFL0, P00579, P0ACK0
- Ligands
- CMP, ZN, MG
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 10 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 | 23% helix, 31% strand | P0A7Z6 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 228 | 21% helix, 32% strand | P0A7Z6 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1340 | 31% helix, 21% strand | B7MIX3 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1337 | 35% helix, 13% strand | P0A8T8 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 79 | 68% helix, 0% strand | B7MFL0 |
| F | RNA polymerase sigma factor rpod | protein | 483 | 64% helix, 0% strand | P00579 |
| G, H | Camp-activated global transcriptional regulator crp | protein | 197 | 37% helix, 25% strand | P0ACK0 |
| 1 | Synthetic nontemplate strand DNA (78-mer) | dna | 78 | — | — |
| 2 | Synthetic template strand DNA (78-mer) | dna | 78 | — | — |
| 3 | Nascent RNA | rna | 3 | — | — |
Ligands and binding sites
- CMP · Adenosine-3',5'-cyclic-monophosphate · ligand · 2 copies · chains G, H
- ZN · Zinc ion · metal · 2 copies · chains D
- MG · Magnesium ion · metal · chains D, 3
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 | 1156 | 0.88 | 0.89 | 144 | empty |
| 2 | 478 | 0.87 | 0.94 | 78 | empty |
| 3 | 655 | 0.86 | 0.91 | 96 | empty |
| 4 | 1066 | 0.86 | 0.87 | 137 | empty |
| 5 | 874 | 0.86 | 0.88 | 104 | empty |
Interfaces
26 interfaces between chains.
- C–D · 7352 Ų buried · 73 hydrogen bonds · protein-protein
- 1–2 · 2794 Ų buried · 229 hydrogen bonds · nucleic-nucleic
- D–F · 1944 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1817 Ų buried · 23 hydrogen bonds · protein-protein
- C–F · 1755 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 6PB4 · The E. coli class-II CAP-dependent transcription activation complex with de novo RNA… · the same entry in another collection · chain 3 against 3, 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 0.96
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 P0ACK0
- Elsewhere: RCSB PDB 6PB4 · PDBe 6PB4 · UniProt P0A7Z6 · UniProt B7MIX3 · UniProt P0A8T8 · UniProt B7MFL0 · UniProt P00579 · UniProt P0ACK0
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