MolNFT v1 · #182220 · protein + DNA
Cryo-EM structure of escherichia COLI RNA polymerase bound to lambda pr promoter DNA (class 2)
7MKE · DNA-directed RNA polymerase subunit alpha: “Cryo-EM structure of escherichia COLI RNA polymerase bound to lambda pr promoter DNA (class 2)”. Electron microscopy, 3 ligands (1N7, ZN, MG), 20 pockets (best druggability 0.84). MolNFT…
- PDB
- 7MKE
- Type
- protein + DNA
- Length
- 3,756 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
- A0A073G207, P0A8V4, A0A4S1NBU2, P0A802, Q0P6L9
- Ligands
- 1N7, ZN, MG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 8 distinct chains · 36% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| G | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 233 | 21% helix, 31% strand | A0A073G207 |
| H | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 223 | 19% helix, 30% strand | A0A073G207 |
| I | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1340 | 30% helix, 21% strand | P0A8V4 |
| J | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1335 | 36% helix, 17% strand | A0A4S1NBU2 |
| K | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 79 | 59% helix, 0% strand | P0A802 |
| L | RNA polymerase sigma factor rpod | protein | 465 | 69% helix, 1% strand | Q0P6L9 |
| P | Nontemplate strand of lambda pr DNA promoter | dna | 44 | — | — |
| Q | Template strand of lambda pr DNA promoter | dna | 37 | — | — |
Ligands and binding sites
- 1N7 · Chapso · ligand · 4 copies · chains I, G, J, L
- ZN · Zinc ion · metal · 2 copies · chains J
- 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 | 912 | 0.84 | 0.85 | 88 | empty |
| 2 | 1061 | 0.79 | 0.81 | 122 | empty |
| 3 | 785 | 0.78 | 0.82 | 83 | empty |
| 4 | 473 | 0.78 | 0.86 | 46 | empty |
| 5 | 729 | 0.78 | 0.82 | 56 | empty |
Interfaces
16 interfaces between chains.
- I–J · 8192 Ų buried · 95 hydrogen bonds · protein-protein
- J–L · 2687 Ų buried · 29 hydrogen bonds · protein-protein
- G–H · 2249 Ų buried · 19 hydrogen bonds · protein-protein
- I–L · 2122 Ų buried · 10 hydrogen bonds · protein-protein
- G–I · 1884 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 7MKE · Cryo-EM structure of Escherichia coli RNA polymerase bound to lambda PR promoter DNA… · the same entry in another collection · chain Q against Q, TM-score 1.00
- P0A802 · AlphaFold monomer V2.0 prediction for DNA-directed RNA polymerase subunit omega (P0A802) · a predicted model of the same protein · chain K against A, TM-score 0.93
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 A0A073G207
- Every structure of UniProt P0A8V4
- Every structure of UniProt A0A4S1NBU2
- Every structure of UniProt P0A802
- Every structure of UniProt Q0P6L9
- Elsewhere: RCSB PDB 7MKE · PDBe 7MKE · UniProt A0A073G207 · UniProt P0A8V4 · UniProt A0A4S1NBU2 · UniProt P0A802 · UniProt Q0P6L9
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