MolNFT v1 · #182230 · protein + DNA + RNA
Escherichia COLI RNA polymerase elongation complex
7MKO · DNA-directed RNA polymerase subunit alpha: “Escherichia COLI RNA polymerase elongation complex”. Electron microscopy, 3 ligands (2TM, ZN, MG), 20 pockets (best druggability 0.86). MolNFT v1 #182230 on GenesisL1: 3D structure…
- PDB
- 7MKO
- Type
- protein + DNA + RNA
- Length
- 3,256 residues
- Chains
- 8
- 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
- 2TM, ZN, MG
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 8 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, 39% strand | A0A4S5AL01 |
| C | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1320 | 32% helix, 22% strand | A0A4S4NK82 |
| D | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1344 | 38% helix, 15% strand | A0A6D2WUT6 |
| E | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 69 | 57% helix, 0% strand | P0A800 |
| N | DNA (29-mer) | dna | 22 | — | — |
| R | RNA (20-mer) | rna | 11 | — | — |
| T | DNA (29-mer) | dna | 29 | — | — |
Ligands and binding sites
- 2TM · 5'-O-[(S)-hydroxy{[(s)-hydroxy(phosphonooxy) phosphoryl]methyl}phosphoryl]cytidine · ligand · chains C, D, R, T
- ZN · Zinc ion · metal · 2 copies · chains D
- MG · Magnesium ion · metal · chains D, R
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 | 898 | 0.86 | 0.89 | 107 | empty |
| 2 | 626 | 0.82 | 0.87 | 63 | empty |
| 3 | 423 | 0.78 | 0.88 | 42 | 2TM |
| 4 | 813 | 0.78 | 0.81 | 77 | empty |
| 5 | 315 | 0.77 | 0.89 | 44 | empty |
Interfaces
15 interfaces between chains.
- C–D · 8041 Ų buried · 108 hydrogen bonds · protein-protein
- A–B · 2158 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 1784 Ų buried · 25 hydrogen bonds · protein-protein
- D–E · 1494 Ų buried · 17 hydrogen bonds · protein-protein
- D–T · 1239 Ų buried · 19 hydrogen bonds · protein-nucleic
Compared structures
- 7MKO · Escherichia coli RNA polymerase elongation complex · 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 7MKO · PDBe 7MKO · UniProt A0A4S5AL01 · UniProt A0A4S4NK82 · UniProt A0A6D2WUT6 · UniProt P0A800
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