MolNFT v2 · #177037 · protein + DNA
Cryo-EM structure of an Escherichia coli RNAP-promoter open complex (RPo) with SspA
7C97 · DNA (63-mer): “Cryo-EM structure of an Escherichia coli RNAP-promoter open complex (RPo) with SspA”. Electron microscopy at 3.68, 2 ligands (ZN, MG), 20 pockets (best druggability 0.83). MolNFT v2 #177037 on GenesisL1: 3D structure…
- PDB
- 7C97
- Type
- protein + DNA
- Length
- 4,275 residues
- Chains
- 11
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.68
- Source
- Escherichia coli; Escherichia coli (strain K12); SYNTHETIC CONSTRUCT
- Molecule
- DNA (63-mer); Stringent starvation protein A; DNA-directed RNA polymerase subunit alpha…
- EC
- 2.5.1.18, 2.7.7.6
- UniProt
- H4IXP2, F4VJT6, P0A8V2, M9GTE2, T9C803, Q0P6L9
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · resolution 3.68 · 11 distinct chains · 32% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | DNA (63-mer) | dna | 63 | — | — |
| I | Stringent starvation protein A (EC 2.5.1.18) | protein | 206 | 50% helix, 2% strand | H4IXP2 |
| J | Stringent starvation protein A (EC 2.5.1.18) | protein | 201 | 50% helix, 6% strand | H4IXP2 |
| K | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 67 | 45% helix, 0% strand | F4VJT6 |
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 230 | 20% helix, 30% strand | F4VJT6 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 226 | 18% helix, 24% strand | F4VJT6 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1340 | 24% helix, 19% strand | P0A8V2 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1343 | 28% helix, 12% strand | M9GTE2 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 79 | 53% helix, 0% strand | T9C803 |
| F | RNA polymerase sigma factor RpoD | protein | 472 | 61% helix, 0% strand | Q0P6L9 |
| G | DNA (63-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 | 978 | 0.83 | 0.85 | 89 | empty |
| 2 | 1116 | 0.79 | 0.81 | 93 | empty |
| 3 | 647 | 0.78 | 0.83 | 62 | empty |
| 4 | 550 | 0.77 | 0.84 | 65 | empty |
| 5 | 1139 | 0.77 | 0.79 | 104 | empty |
Interfaces
24 interfaces between chains.
- C–D · 7954 Ų buried · 67 hydrogen bonds · protein-protein
- D–F · 2707 Ų buried · 18 hydrogen bonds · protein-protein
- H–G · 2469 Ų buried · 185 hydrogen bonds · nucleic-nucleic
- A–B · 2128 Ų buried · 8 hydrogen bonds · protein-protein
- C–F · 2115 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 7C97 · Cryo-EM structure of an escherichia COLI rnap-promoter open complex (rpo) with sspa · the same entry in another collection · chain K against K, 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
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 H4IXP2
- Every structure of UniProt F4VJT6
- Every structure of UniProt P0A8V2
- Every structure of UniProt M9GTE2
- Every structure of UniProt T9C803
- Every structure of UniProt Q0P6L9
- Elsewhere: RCSB PDB 7C97 · PDBe 7C97 · UniProt H4IXP2 · UniProt F4VJT6 · UniProt P0A8V2 · UniProt M9GTE2 · UniProt T9C803 · UniProt Q0P6L9
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