MolNFT v1 · #160730 · protein + DNA
Escherichia COLI RNA polymerase promoter unwinding intermediate (TRPI1.5B) with trar and mutant rpst P2 promoter
6PST · Protein trar: “Escherichia COLI RNA polymerase promoter unwinding intermediate (TRPI1.5B) with trar and mutant rpst P2…”. Electron microscopy, 3 ligands (1N7, ZN, MG), 20 pockets (best druggability 0.84). MolNFT v1 #160730 on…
- PDB
- 6PST
- Type
- protein + DNA
- Length
- 3,827 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein trar; DNA (85-mer); DNA-directed RNA polymerase subunit alpha; DNA-directed RNA…
- EC
- 2.7.7.6
- UniProt
- P41065, P0A7Z4, P0A8V4, P0A8T7, P0A802, Q0P6L9
- Ligands
- 1N7, ZN, MG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 10 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| N | Protein trar | protein | 72 | 54% helix, 0% strand | P41065 |
| O | DNA (85-mer) | dna | 50 | — | — |
| P | DNA (85-mer) | dna | 51 | — | — |
| M | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 73 | 44% helix, 0% strand | P0A7Z4 |
| G | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 232 | 22% helix, 40% strand | P0A7Z4 |
| H | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 218 | 20% helix, 37% strand | P0A7Z4 |
| I | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1337 | 29% helix, 23% strand | P0A8V4 |
| J | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1164 | 41% helix, 16% strand | P0A8T7 |
| K | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 72 | 68% helix, 0% strand | P0A802 |
| L | RNA polymerase sigma factor rpod | protein | 558 | 66% helix, 1% strand | Q0P6L9 |
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 | 1042 | 0.84 | 0.85 | 92 | empty |
| 2 | 835 | 0.79 | 0.82 | 117 | MG |
| 3 | 1079 | 0.77 | 0.79 | 90 | empty |
| 4 | 491 | 0.76 | 0.85 | 56 | empty |
| 5 | 124 | 0.76 | 0.95 | 28 | empty |
Interfaces
21 interfaces between chains.
- I–J · 8173 Ų buried · 97 hydrogen bonds · protein-protein
- J–L · 3898 Ų buried · 32 hydrogen bonds · protein-protein
- I–L · 2561 Ų buried · 23 hydrogen bonds · protein-protein
- G–H · 2181 Ų buried · 16 hydrogen bonds · protein-protein
- O–P · 2094 Ų buried · 161 hydrogen bonds · nucleic-nucleic
Compared structures
- 6PST · Escherichia coli RNA polymerase promoter unwinding intermediate (TRPi1.5b) with TraR and… · the same entry in another collection · chain L against L, 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 0.77
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 6PST · PDBe 6PST · UniProt P41065 · UniProt P0A7Z4 · UniProt P0A8V4 · UniProt P0A8T7 · UniProt P0A802 · UniProt Q0P6L9
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