Research workbench
Escherichia COLI RNA polymerase promoter unwinding intermediate (TRPI2) with trar and rpst P2 promoter
Analyse Escherichia COLI RNA polymerase promoter unwinding intermediate (TRPI2) with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PSU
- Type
- protein + DNA
- Length
- 3,956 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein trar; DNA-directed RNA polymerase subunit alpha; DNA-directed RNA polymerase…
- EC
- 2.7.7.6
- UniProt
- P41065, P0A7Z4, P0A8V4, P0A8T7, P0A802, Q0P6L9
- Ligands
- 1N7, ZN, MG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 10 distinct chains · 36% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| N | Protein trar | protein | 72 | 56% helix, 6% strand | P41065 |
| G | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 230 | 22% helix, 30% strand | P0A7Z4 |
| H | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 217 | 21% helix, 25% strand | P0A7Z4 |
| I | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1340 | 29% helix, 19% strand | P0A8V4 |
| J | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1344 | 35% helix, 13% strand | P0A8T7 |
| K | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 72 | 57% helix, 0% strand | P0A802 |
| L | RNA polymerase sigma factor rpod | protein | 529 | 62% helix, 1% strand | Q0P6L9 |
| O | DNA (85-mer) | dna | 42 | — | — |
| P | DNA (85-mer) | dna | 37 | — | — |
| M | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 73 | 51% helix, 0% strand | P0A7Z4 |
Ligands and binding sites
- 1N7 · Chapso · ligand · 4 copies · chains N, J, G, I, L
- ZN · Zinc ion · metal · 3 copies · chains N, J
- MG · Magnesium ion · metal · chains J
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 | 994 | 0.85 | 0.86 | 100 | empty |
| 2 | 980 | 0.79 | 0.81 | 94 | empty |
| 3 | 1023 | 0.79 | 0.81 | 96 | empty |
| 4 | 565 | 0.79 | 0.85 | 75 | empty |
| 5 | 830 | 0.78 | 0.81 | 83 | empty |
Interfaces
20 interfaces between chains.
- I–J · 8138 Ų buried · 103 hydrogen bonds · protein-protein
- J–L · 3228 Ų buried · 31 hydrogen bonds · protein-protein
- I–L · 2394 Ų buried · 20 hydrogen bonds · protein-protein
- G–H · 2026 Ų buried · 12 hydrogen bonds · protein-protein
- G–I · 1862 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 6PSU · Escherichia coli RNA polymerase promoter unwinding intermediate (TRPi2) with TraR and… · the same entry in another collection · chain M against M, TM-score 1.00
- P0A802 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit omega (P0A802) · a predicted model of the same protein · chain K against A, TM-score 0.92
- P41065 · AlphaFold monomer V2.0 prediction for protein trar (P41065) · a predicted model of the same protein · chain N against A, TM-score 0.80
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 P41065
- Every structure of UniProt P0A7Z4
- Every structure of UniProt P0A8V4
- Every structure of UniProt P0A8T7
- Every structure of UniProt P0A802
- Every structure of UniProt Q0P6L9
- Elsewhere: RCSB PDB 6PSU · PDBe 6PSU · UniProt P41065 · UniProt P0A7Z4 · UniProt P0A8V4 · UniProt P0A8T7 · UniProt P0A802 · UniProt Q0P6L9
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