MolNFT v1 · #154681 · protein + DNA + RNA
Cryo-EM structure of escherichia COLI crl transcription activation complex
6KJ6 · DNA-directed RNA polymerase subunit alpha: “Cryo-EM structure of escherichia COLI crl transcription activation complex”. Electron microscopy, 2 ligands (ZN, MG), 20 pockets (best druggability 0.81). MolNFT v1 #154681 on GenesisL1…
- PDB
- 6KJ6
- Type
- protein + DNA + RNA
- Length
- 3,591 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
- P0A7Z4, P0A8V2, P0A8T7, P0A800, P13445, B1J0Z4
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 10 distinct chains · 21% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 218 | 8% helix, 21% strand | P0A7Z4 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 227 | 13% helix, 22% strand | P0A7Z4 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1327 | 18% helix, 16% strand | P0A8V2 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1265 | 19% helix, 13% strand | P0A8T7 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 74 | 36% helix, 0% strand | P0A800 |
| F | RNA polymerase sigma factor rpos | protein | 277 | 49% helix, 1% strand | P13445 |
| G | DNA (51-mer) | dna | 46 | — | — |
| H | DNA (51-mer) | dna | 46 | — | — |
| I | RNA (5'-R(*CP*UP*CP*GP*A)-3') | rna | 5 | — | — |
| J | Sigma factor-binding protein crl | protein | 106 | 28% helix, 18% strand | B1J0Z4 |
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 | 1080 | 0.81 | 0.82 | 113 | empty |
| 2 | 927 | 0.80 | 0.82 | 78 | empty |
| 3 | 634 | 0.80 | 0.86 | 52 | empty |
| 4 | 991 | 0.79 | 0.81 | 118 | empty |
| 5 | 575 | 0.79 | 0.85 | 58 | empty |
Interfaces
22 interfaces between chains.
- C–D · 7630 Ų buried · 57 hydrogen bonds · protein-protein
- C–F · 2048 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 1750 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 1685 Ų buried · 12 hydrogen bonds · protein-protein
- D–F · 1615 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6KJ6 · cryo-EM structure of Escherichia coli Crl transcription activation complex · the same entry in another collection · chain G against G, 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 0.98
- P13445 · AlphaFold monomer V2.0 prediction for RNA polymerase sigma factor rpos (P13445) · a predicted model of the same protein · chain F against A, TM-score 0.95
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 P13445
- Every structure of UniProt B1J0Z4
- Elsewhere: RCSB PDB 6KJ6 · PDBe 6KJ6 · UniProt P0A7Z4 · UniProt P0A8V2 · UniProt P0A8T7 · UniProt P0A800 · UniProt P13445 · UniProt B1J0Z4
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