MolNFT v1 · #182224 · protein + DNA
Cryo-EM structure of escherichia COLI RNA polymerase bound to lambda pr (-5G to C) promoter DNA
7MKI · Nontemplate strand of lambda pr DNA promoter (-5G to C): “Cryo-EM structure of escherichia COLI RNA polymerase bound to lambda pr (-5G to C) promoter DNA”. Electron microscopy, 3 ligands (1N7, ZN, MG), 20 pockets (best druggability…
- PDB
- 7MKI
- Type
- protein + DNA
- Length
- 3,772 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nontemplate strand of lambda pr DNA promoter (-5G to C); DNA-directed RNA polymerase…
- EC
- 2.7.7.6
- UniProt
- A0A073G207, P0A8V4, A0A4S1NBU2, P0A802, Q0P6L9
- Ligands
- 1N7, ZN, MG
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 8 distinct chains · 35% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P | Nontemplate strand of lambda pr DNA promoter (-5G to C) | dna | 49 | — | — |
| G | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 233 | 19% helix, 32% strand | A0A073G207 |
| H | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 223 | 18% helix, 30% strand | A0A073G207 |
| I | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1340 | 27% helix, 21% strand | P0A8V4 |
| J | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1335 | 34% helix, 16% strand | A0A4S1NBU2 |
| K | DNA-directed RNA polymerase subunit omega (EC 2.7.7.6) | protein | 79 | 63% helix, 0% strand | P0A802 |
| L | RNA polymerase sigma factor rpod | protein | 466 | 68% helix, 1% strand | Q0P6L9 |
| Q | Template strand of lambda pr promoter DNA (-5C to G) | dna | 47 | — | — |
Ligands and binding sites
- 1N7 · Chapso · ligand · 3 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 | 882 | 0.82 | 0.84 | 84 | empty |
| 2 | 706 | 0.82 | 0.86 | 97 | empty |
| 3 | 835 | 0.81 | 0.84 | 75 | empty |
| 4 | 1085 | 0.81 | 0.82 | 103 | 1N7 |
| 5 | 1067 | 0.78 | 0.80 | 90 | empty |
Interfaces
16 interfaces between chains.
- I–J · 8228 Ų buried · 88 hydrogen bonds · protein-protein
- J–L · 2814 Ų buried · 22 hydrogen bonds · protein-protein
- I–L · 2369 Ų buried · 16 hydrogen bonds · protein-protein
- G–H · 2216 Ų buried · 10 hydrogen bonds · protein-protein
- G–I · 1794 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 7MKI · Cryo-EM structure of Escherichia coli RNA polymerase bound to lambda PR (-5G to C)… · 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 7MKI · PDBe 7MKI · UniProt A0A073G207 · UniProt P0A8V4 · UniProt A0A4S1NBU2 · UniProt P0A802 · UniProt Q0P6L9
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