MolNFT v1 · #153349 · protein + DNA + RNA
Cryoem structure of escherichia COLI sigmae transcription initiation complex containing 5NT of RNA
6JBQ · DNA-directed RNA polymerase subunit alpha: “Cryoem structure of escherichia COLI sigmae transcription initiation complex containing 5NT of RNA”. Electron microscopy, 2 ligands (ZN, MG), 20 pockets (best druggability 0.84). MolNFT v1…
- PDB
- 6JBQ
- Type
- protein + DNA + RNA
- Length
- 3,448 residues
- Chains
- 9
- 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, P0AGB6
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 9 distinct chains · 31% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 216 | 17% helix, 31% strand | P0A7Z4 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 219 | 18% helix, 43% strand | P0A7Z4 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1312 | 28% helix, 23% strand | P0A8V2 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1335 | 33% helix, 16% strand | P0A8T7 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 79 | 59% helix, 0% strand | P0A800 |
| F | Ecf RNA polymerase sigma-E factor | protein | 186 | 63% helix, 2% strand | P0AGB6 |
| G | DNA (48-mer) | dna | 48 | — | — |
| H | DNA (48-mer) | dna | 48 | — | — |
| I | RNA (5'-R(*CP*UP*CP*GP*A)-3') | rna | 5 | — | — |
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 | 946 | 0.84 | 0.86 | 88 | empty |
| 2 | 1140 | 0.83 | 0.84 | 91 | empty |
| 3 | 902 | 0.82 | 0.84 | 96 | empty |
| 4 | 827 | 0.81 | 0.84 | 77 | empty |
| 5 | 712 | 0.81 | 0.85 | 61 | empty |
Interfaces
19 interfaces between chains.
- C–D · 8609 Ų buried · 78 hydrogen bonds · protein-protein
- D–F · 2046 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1771 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1674 Ų buried · 10 hydrogen bonds · protein-protein
- C–F · 1655 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6JBQ · CryoEM structure of Escherichia coli sigmaE transcription initiation complex containing… · the same entry in another collection · chain I against I, 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
- P0AGB6 · AlphaFold monomer V2.0 prediction for ecf RNA polymerase sigma-E factor (P0AGB6) · a predicted model of the same protein · chain F against A, TM-score 0.45
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 P0AGB6
- Elsewhere: RCSB PDB 6JBQ · PDBe 6JBQ · UniProt P0A7Z4 · UniProt P0A8V2 · UniProt P0A8T7 · UniProt P0A800 · UniProt P0AGB6
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