Research workbench
Cryo-EM structure of escherichia COLI rnap polymerase bound with trar in conformation II
Analyse Cryo-EM structure of escherichia COLI rnap polymerase bound with trar in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6N58
- Type
- protein
- Length
- 3,833 residues
- Chains
- 7
- 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, P0A8V2, P0A8T7, P0A800, Q0P6L9, P41065
- Ligands
- 1N7, ZN, MG
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 7 distinct chains · 37% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 228 | 22% helix, 32% strand | P0A7Z4 |
| H | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 219 | 19% helix, 25% strand | P0A7Z4 |
| I | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1341 | 29% helix, 20% strand | P0A8V2 |
| J | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1347 | 35% helix, 14% strand | P0A8T7 |
| K | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 79 | 62% helix, 0% strand | P0A800 |
| L | RNA polymerase sigma factor rpod | protein | 547 | 65% helix, 0% strand | Q0P6L9 |
| M | Protein trar | protein | 72 | 57% helix, 0% strand | P41065 |
Ligands and binding sites
- 1N7 · Chapso · ligand · 4 copies · chains G, I, J, L, M
- ZN · Zinc ion · metal · 3 copies · chains J, M
- 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 | 607 | 0.82 | 0.87 | 57 | empty |
| 2 | 556 | 0.78 | 0.85 | 63 | empty |
| 3 | 1071 | 0.78 | 0.80 | 111 | empty |
| 4 | 901 | 0.78 | 0.81 | 82 | empty |
| 5 | 1099 | 0.78 | 0.80 | 83 | empty |
Interfaces
11 interfaces between chains.
- I–J · 8480 Ų buried · 97 hydrogen bonds · protein-protein
- J–L · 3530 Ų buried · 29 hydrogen bonds · protein-protein
- I–L · 2602 Ų buried · 4 hydrogen bonds · protein-protein
- J–M · 2175 Ų buried · 9 hydrogen bonds · protein-protein
- G–I · 1988 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6N58 · Cryo-EM structure of Escherichia coli RNAP polymerase bound with TraR in conformation II · the same entry in another collection · chain M against M, 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 I against A, TM-score 0.93
- P41065 · AlphaFold monomer V2.0 prediction for protein trar (P41065) · a predicted model of the same protein · chain M 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 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 P41065
- Elsewhere: RCSB PDB 6N58 · PDBe 6N58 · UniProt P0A7Z4 · UniProt P0A8V2 · UniProt P0A8T7 · UniProt P0A800 · UniProt Q0P6L9 · UniProt P41065
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