Research workbench
Escherichia COLI RNA polymerase SIGMA70-holoenzyme bound to upstream fork promoter DNA and microcin J25 (MCCJ25)
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
- 6N60
- Type
- protein + DNA
- Length
- 3,491 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, Q9X2V7
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 9 distinct chains · 36% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 231 | 19% helix, 29% strand | P0A7Z4 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 218 | 20% helix, 32% strand | P0A7Z4 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1335 | 31% helix, 22% strand | P0A8V2 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1236 | 39% helix, 16% 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 | 318 | 67% helix, 2% strand | Q0P6L9 |
| M | Microcin J25 | protein | 21 | 0% helix, 19% strand | Q9X2V7 |
| N | Non-template strand DNA | dna | 29 | — | — |
| T | Template strand DNA | dna | 24 | — | — |
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 | 1137 | 0.85 | 0.86 | 110 | empty |
| 2 | 1023 | 0.78 | 0.80 | 108 | MG |
| 3 | 1110 | 0.77 | 0.80 | 81 | empty |
| 4 | 1020 | 0.77 | 0.79 | 84 | empty |
| 5 | 616 | 0.76 | 0.82 | 71 | empty |
Interfaces
16 interfaces between chains.
- C–D · 8500 Ų buried · 115 hydrogen bonds · protein-protein
- D–F · 2484 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 1919 Ų buried · 26 hydrogen bonds · protein-protein
- C–F · 1891 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1697 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 6N60 · Escherichia coli RNA polymerase sigma70-holoenzyme bound to upstream fork promoter DNA… · the same entry in another collection · chain T against T, 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
- Q9X2V7 · AlphaFold monomer V2.0 prediction for microcin J25 (Q9X2V7) · a predicted model of the same protein · chain M against A, TM-score 0.19
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 Q9X2V7
- Elsewhere: RCSB PDB 6N60 · PDBe 6N60 · UniProt P0A7Z4 · UniProt P0A8V2 · UniProt P0A8T7 · UniProt P0A800 · UniProt Q0P6L9 · UniProt Q9X2V7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.