MolNFT v1 · #176807 · protein + DNA
A refined cryo-EM structure of an escherichia COLI rnap-promoter open complex (rpo) with sspa
7DY6 · DNA (63-mer): “A refined cryo-EM structure of an escherichia COLI rnap-promoter open complex (rpo) with sspa”. Electron microscopy, 2 ligands (ZN, MG), 20 pockets (best druggability 0.80). MolNFT v1 #176807 on GenesisL1: 3D…
- PDB
- 7DY6
- Type
- protein + DNA
- Length
- 4,298 residues
- Chains
- 11
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (63-mer); Stringent starvation protein a; DNA-directed RNA polymerase subunit alpha…
- EC
- 2.7.7.6
- UniProt
- P0ACA3, A0A4S5AL01, P0A8V2, P0A8T7, P00579, A0A4S5AUM4
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 11 distinct chains · 29% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | DNA (63-mer) | dna | 63 | — | — |
| I | Stringent starvation protein a | protein | 206 | 44% helix, 2% strand | P0ACA3 |
| J | Stringent starvation protein a | protein | 201 | 45% helix, 4% strand | P0ACA3 |
| K | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 67 | 40% helix, 0% strand | A0A4S5AL01 |
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 230 | 18% helix, 25% strand | A0A4S5AL01 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 226 | 16% helix, 23% strand | A0A4S5AL01 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1340 | 21% helix, 17% strand | P0A8V2 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1355 | 27% helix, 12% strand | P0A8T7 |
| F | RNA polymerase sigma factor rpod | protein | 472 | 52% helix, 0% strand | P00579 |
| G | DNA (63-mer) | dna | 48 | — | — |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 90 | 54% helix, 0% strand | A0A4S5AUM4 |
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 | 727 | 0.80 | 0.84 | 60 | empty |
| 2 | 923 | 0.79 | 0.82 | 78 | empty |
| 3 | 593 | 0.77 | 0.84 | 58 | empty |
| 4 | 743 | 0.77 | 0.82 | 68 | empty |
| 5 | 1045 | 0.77 | 0.79 | 92 | empty |
Interfaces
25 interfaces between chains.
- C–D · 7982 Ų buried · 65 hydrogen bonds · protein-protein
- D–F · 2696 Ų buried · 19 hydrogen bonds · protein-protein
- H–G · 2486 Ų buried · 197 hydrogen bonds · nucleic-nucleic
- C–F · 2118 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 2117 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 7DY6 · A refined cryo-EM structure of an Escherichia coli RNAP-promoter open complex (RPo) with… · the same entry in another collection · chain E against E, TM-score 1.00
- P0ACA3 · AlphaFold monomer V2.0 prediction for stringent starvation protein a (P0ACA3) · a predicted model of the same protein · chain I 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 P0ACA3
- Every structure of UniProt A0A4S5AL01
- Every structure of UniProt P0A8V2
- Every structure of UniProt P0A8T7
- Every structure of UniProt P00579
- Every structure of UniProt A0A4S5AUM4
- Elsewhere: RCSB PDB 7DY6 · PDBe 7DY6 · UniProt P0ACA3 · UniProt A0A4S5AL01 · UniProt P0A8V2 · UniProt P0A8T7 · UniProt P00579 · UniProt A0A4S5AUM4
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