Research workbench
Escherichia COLI RNA polymerase promoter unwinding intermediate (TRPI1.5A) with trar and mutant rpst P2 promoter
Analyse Escherichia COLI RNA polymerase promoter unwinding intermediate (TRPI1.5A) with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PSS
- Type
- protein + DNA
- Length
- 3,991 residues
- Chains
- 10
- Method
- electron microscopy
- 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, P0A8V4, P0A8T7, P0A802, Q0P6L9, P41065
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 10 distinct chains · 35% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 232 | 20% helix, 34% strand | P0A7Z4 |
| H | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 218 | 17% helix, 30% strand | P0A7Z4 |
| I | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1337 | 28% helix, 22% strand | P0A8V4 |
| J | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1343 | 34% helix, 18% strand | P0A8T7 |
| K | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 72 | 67% helix, 0% strand | P0A802 |
| L | RNA polymerase sigma factor rpod | protein | 558 | 60% helix, 1% strand | Q0P6L9 |
| M | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 73 | 44% helix, 0% strand | P0A7Z4 |
| N | Protein trar | protein | 72 | 53% helix, 3% strand | P41065 |
| O | DNA (85-mer) | dna | 43 | — | — |
| P | DNA (85-mer) | dna | 43 | — | — |
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 | 581 | 0.82 | 0.87 | 58 | empty |
| 2 | 813 | 0.80 | 0.83 | 96 | empty |
| 3 | 707 | 0.78 | 0.82 | 80 | empty |
| 4 | 1156 | 0.77 | 0.79 | 92 | empty |
| 5 | 988 | 0.76 | 0.79 | 87 | MG |
Interfaces
21 interfaces between chains.
- I–J · 8237 Ų buried · 111 hydrogen bonds · protein-protein
- J–L · 3939 Ų buried · 32 hydrogen bonds · protein-protein
- I–L · 2801 Ų buried · 22 hydrogen bonds · protein-protein
- G–H · 2235 Ų buried · 21 hydrogen bonds · protein-protein
- O–P · 1931 Ų buried · 157 hydrogen bonds · nucleic-nucleic
Compared structures
- 6PSS · Escherichia coli RNA polymerase promoter unwinding intermediate (TRPi1.5a) with TraR and… · the same entry in another collection · chain P against P, 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 0.96
- P41065 · AlphaFold monomer V2.0 prediction for protein trar (P41065) · a predicted model of the same protein · chain N against A, TM-score 0.78
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 P0A8V4
- Every structure of UniProt P0A8T7
- Every structure of UniProt P0A802
- Every structure of UniProt Q0P6L9
- Every structure of UniProt P41065
- Elsewhere: RCSB PDB 6PSS · PDBe 6PSS · UniProt P0A7Z4 · UniProt P0A8V4 · UniProt P0A8T7 · UniProt P0A802 · UniProt Q0P6L9 · UniProt P41065
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