Research workbench
Escherichia COLI RNA polymerase core enzyme
Analyse Escherichia COLI RNA polymerase core enzyme in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MKP
- Type
- protein
- Length
- 3,193 residues
- Chains
- 5
- 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
- A0A4S5AL01, A0A4S4NK82, A0A6D2WUT6, P0A800
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 5 distinct chains · 33% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 231 | 24% helix, 39% strand | A0A4S5AL01 |
| B | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 230 | 21% helix, 40% strand | A0A4S5AL01 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1323 | 32% helix, 22% strand | A0A4S4NK82 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1340 | 37% helix, 15% strand | A0A6D2WUT6 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 69 | 57% helix, 0% strand | P0A800 |
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 | 657 | 0.82 | 0.87 | 67 | empty |
| 2 | 147 | 0.80 | 0.96 | 25 | empty |
| 3 | 926 | 0.80 | 0.82 | 83 | empty |
| 4 | 348 | 0.77 | 0.88 | 53 | empty |
| 5 | 803 | 0.75 | 0.79 | 80 | empty |
Interfaces
7 interfaces between chains.
- C–D · 7339 Ų buried · 58 hydrogen bonds · protein-protein
- A–B · 1997 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 1594 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 1379 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 1012 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 7MKP · Escherichia coli RNA polymerase core enzyme · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A4S5AL01
- Every structure of UniProt A0A4S4NK82
- Every structure of UniProt A0A6D2WUT6
- Every structure of UniProt P0A800
- Elsewhere: RCSB PDB 7MKP · PDBe 7MKP · UniProt A0A4S5AL01 · UniProt A0A4S4NK82 · UniProt A0A6D2WUT6 · UniProt P0A800
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