MolNFT v1 · #182232 · protein
Escherichia COLI RNA polymerase and rapa binary complex
7MKQ · DNA-directed RNA polymerase subunit alpha: “Escherichia COLI RNA polymerase and rapa binary complex”. Electron microscopy, 2 ligands (ZN, MG), 20 pockets (best druggability 0.83). MolNFT v1 #182232 on GenesisL1: 3D structure…
- PDB
- 7MKQ
- Type
- protein
- Length
- 4,182 residues
- Chains
- 6
- 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, 3.6.4.-
- UniProt
- A0A4S5AL01, A0A4S4NK82, A0A6D2WUT6, P0A800, P60240
- Ligands
- ZN, MG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 6 distinct chains · 36% helix, 20% 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, 38% 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 | 1340 | 32% helix, 21% strand | A0A4S4NK82 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1338 | 37% helix, 16% strand | A0A6D2WUT6 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 76 | 61% helix, 0% strand | P0A800 |
| L | RNA polymerase-associated protein rapa (EC 3.6.4.-) | protein | 967 | 46% helix, 16% strand | P60240 |
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 | 930 | 0.83 | 0.85 | 86 | empty |
| 2 | 1165 | 0.80 | 0.82 | 95 | empty |
| 3 | 819 | 0.79 | 0.82 | 95 | empty |
| 4 | 903 | 0.77 | 0.80 | 85 | empty |
| 5 | 699 | 0.76 | 0.81 | 62 | empty |
Interfaces
11 interfaces between chains.
- C–D · 7995 Ų buried · 91 hydrogen bonds · protein-protein
- A–B · 1909 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 1653 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 1309 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 1018 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 7MKQ · Escherichia coli RNA polymerase and RapA binary complex · the same entry in another collection · chain C against C, TM-score 1.00
- P60240 · AlphaFold monomer V2.0 prediction for RNA polymerase-associated protein rapa (P60240) · a predicted model of the same protein · chain L against A, TM-score 0.84
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
- Every structure of UniProt P60240
- Elsewhere: RCSB PDB 7MKQ · PDBe 7MKQ · UniProt A0A4S5AL01 · UniProt A0A4S4NK82 · UniProt A0A6D2WUT6 · UniProt P0A800 · UniProt P60240
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