Research workbench
Escherichia COLI RNA polymerase SIGMA70-holoenzyme bound to upstream fork promoter DNA and capistruin
Analyse Escherichia COLI RNA polymerase SIGMA70-holoenzyme bound to upstream fork… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6N61
- Type
- protein + DNA
- Length
- 3,560 residues
- Chains
- 9
- Method
- x-ray diffraction
- 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, Q0P6L9, A0A096YQF1
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 9 distinct chains · 37% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 228 | 21% helix, 36% strand | P0A7Z4 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 217 | 19% helix, 31% strand | P0A7Z4 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1332 | 30% helix, 22% strand | P0A8V2 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1239 | 39% helix, 15% strand | P0A8T7 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 79 | 59% helix, 0% strand | P0A800 |
| F | RNA polymerase sigma factor rpod | protein | 395 | 69% helix, 2% strand | Q0P6L9 |
| N | Non-template strand DNA | dna | 29 | — | — |
| T | Template strand DNA | dna | 24 | — | — |
| I | Capistruin | protein | 17 | 0% helix, 29% strand | A0A096YQF1 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains D
- MG · Magnesium ion · metal · chains D
- EDO · 1,2-ethanediol · additive · chains C
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains D
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 | 971 | 0.83 | 0.85 | 105 | empty |
| 2 | 1114 | 0.78 | 0.80 | 100 | empty |
| 3 | 916 | 0.77 | 0.80 | 84 | empty |
| 4 | 613 | 0.77 | 0.83 | 65 | empty |
| 5 | 1168 | 0.76 | 0.79 | 97 | EDO |
Interfaces
15 interfaces between chains.
- C–D · 8339 Ų buried · 110 hydrogen bonds · protein-protein
- D–F · 2631 Ų buried · 28 hydrogen bonds · protein-protein
- C–F · 2231 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 1800 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 1722 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6N61 · Escherichia coli RNA polymerase sigma70-holoenzyme bound to upstream fork promoter DNA… · 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
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 Q0P6L9
- Every structure of UniProt A0A096YQF1
- Elsewhere: RCSB PDB 6N61 · PDBe 6N61 · UniProt P0A7Z4 · UniProt P0A8V2 · UniProt P0A8T7 · UniProt P0A800 · UniProt Q0P6L9 · UniProt A0A096YQF1
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