MolNFT v1 · #157618 · protein
Cryo-EM structure of escherichia COLI rnap polymerase bound with trar in conformation I
6N57 · DNA-directed RNA polymerase subunit alpha: “Cryo-EM structure of escherichia COLI rnap polymerase bound with trar in conformation I”. Electron microscopy, 3 ligands (1N7, ZN, MG), 20 pockets (best druggability 0.81). MolNFT v1…
- PDB
- 6N57
- Type
- protein
- Length
- 3,841 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 0.81
Structure
electron microscopy · 7 distinct chains · 36% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 228 | 21% helix, 21% strand | P0A7Z4 |
| H | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 219 | 21% helix, 23% strand | P0A7Z4 |
| I | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1341 | 27% helix, 17% strand | P0A8V2 |
| J | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1347 | 34% 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 | 555 | 66% helix, 1% strand | Q0P6L9 |
| M | Protein trar | protein | 72 | 54% helix, 0% strand | P41065 |
Ligands and binding sites
- 1N7 · Chapso · ligand · 4 copies · chains I, J, L, M
- ZN · Zinc ion · metal · 3 copies · chains J, M
- MG · Magnesium ion · metal · chains J, M
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 | 564 | 0.81 | 0.87 | 54 | empty |
| 2 | 771 | 0.81 | 0.84 | 97 | empty |
| 3 | 1095 | 0.79 | 0.81 | 86 | empty |
| 4 | 557 | 0.78 | 0.85 | 62 | empty |
| 5 | 636 | 0.77 | 0.83 | 74 | empty |
Interfaces
11 interfaces between chains.
- I–J · 8500 Ų buried · 91 hydrogen bonds · protein-protein
- J–L · 3664 Ų buried · 30 hydrogen bonds · protein-protein
- I–L · 2717 Ų buried · 9 hydrogen bonds · protein-protein
- G–H · 2035 Ų buried · 10 hydrogen bonds · protein-protein
- G–I · 2020 Ų buried · 23 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6N57 · Cryo-EM structure of Escherichia coli RNAP polymerase bound with TraR in conformation I · 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 6N57 · PDBe 6N57 · UniProt P0A7Z4 · UniProt P0A8V2 · UniProt P0A8T7 · UniProt P0A800 · UniProt Q0P6L9 · UniProt P41065
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