MolNFT v1 · #182219 · protein + DNA
Cryo-EM structure of escherichia COLI RNA polymerase bound to lambda pr promoter DNA (class 1)
7MKD · DNA-directed RNA polymerase subunit alpha: “Cryo-EM structure of escherichia COLI RNA polymerase bound to lambda pr promoter DNA (class 1)”. Electron microscopy, 3 ligands (1N7, ZN, MG), 20 pockets (best druggability 0.86). MolNFT…
- PDB
- 7MKD
- Type
- protein + DNA
- Length
- 3,894 residues
- Chains
- 9
- 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 0.86
Structure
electron microscopy · 9 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, 32% strand | A0A073G207 |
| H | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 223 | 19% helix, 32% strand | A0A073G207 |
| I | DNA-directed RNA polymerase subunit beta (EC 2.7.7.6) | protein | 1340 | 29% helix, 22% strand | P0A8V4 |
| J | DNA-directed RNA polymerase subunit beta' (EC 2.7.7.6) | protein | 1336 | 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 | 474 | 66% helix, 1% strand | Q0P6L9 |
| P | Nontemplate strand of lambda pr promoter DNA | dna | 68 | — | — |
| Q | Template strand of lambda pr promoter DNA | dna | 68 | — | — |
| R | DNA-directed RNA polymerase subunit alpha (EC 2.7.7.6) | protein | 73 | 51% helix, 3% strand | A0A073G207 |
Ligands and binding sites
- 1N7 · Chapso · ligand · 3 copies · chains I, G, J, L, Q
- 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 | 835 | 0.86 | 0.88 | 105 | empty |
| 2 | 1066 | 0.85 | 0.86 | 105 | empty |
| 3 | 998 | 0.84 | 0.85 | 93 | empty |
| 4 | 685 | 0.76 | 0.82 | 69 | 1N7 |
| 5 | 397 | 0.75 | 0.85 | 49 | empty |
Interfaces
19 interfaces between chains.
- I–J · 8026 Ų buried · 77 hydrogen bonds · protein-protein
- J–L · 2663 Ų buried · 13 hydrogen bonds · protein-protein
- I–L · 2483 Ų buried · 14 hydrogen bonds · protein-protein
- P–Q · 2477 Ų buried · 175 hydrogen bonds · nucleic-nucleic
- G–H · 2107 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7MKD · Cryo-EM structure of Escherichia coli RNA polymerase bound to lambda PR promoter DNA… · the same entry in another collection · chain R against R, 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 0.94
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 7MKD · PDBe 7MKD · UniProt A0A073G207 · UniProt P0A8V4 · UniProt A0A4S1NBU2 · UniProt P0A802 · UniProt Q0P6L9
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