MolNFT v1 · #188904 · protein
Structure of the phage AR9 non-virion RNA polymerase holoenzyme in complex with two DNA oligonucleotides containing the AR9 P077 promoter as determined by cryo-EM
7UM0 · DNA-directed RNA polymerase subunit: “Structure of the phage AR9 non-virion RNA polymerase holoenzyme in complex with two DNA oligonucleotides…”. Electron microscopy, 3 ligands (DU, DG, ZN), 20 pockets (best druggability 0.82).…
- PDB
- 7UM0
- Type
- protein
- Length
- 2,647 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-directed RNA polymerase subunit; DNA-directed RNA polymerase beta' subunit…
- EC
- 2.7.7.6
- UniProt
- A0A172JIC8, A0A172JIH0, A0A172JI16, A0A172JI62, A0A172JHZ2
- Ligands
- DU, DG, ZN
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 5 distinct chains · 39% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit | protein | 459 | 59% helix, 4% strand | A0A172JIC8 |
| d | DNA-directed RNA polymerase beta' subunit | protein | 426 | 34% helix, 14% strand | A0A172JIH0 |
| c | DNA-directed RNA polymerase beta subunit | protein | 484 | 34% helix, 19% strand | A0A172JI16 |
| D | DNA-directed RNA polymerase (EC 2.7.7.6) | protein | 629 | 43% helix, 11% strand | A0A172JI62 |
| C | DNA-directed RNA polymerase (EC 2.7.7.6) | protein | 649 | 30% helix, 21% strand | A0A172JHZ2 |
Ligands and binding sites
- DU · 2'-deoxyuridine-5'-monophosphate · ligand · 2 copies · chains A, c
- DG · 2'-deoxyguanosine-5'-monophosphate · ligand · chains A
- ZN · Zinc ion · metal · chains D
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 | 0.82 | 0.84 | 81 | empty |
| 2 | 461 | 0.79 | 0.87 | 47 | empty |
| 3 | 805 | 0.78 | 0.81 | 59 | empty |
| 4 | 440 | 0.78 | 0.86 | 31 | empty |
| 5 | 138 | 0.77 | 0.95 | 29 | empty |
Interfaces
8 interfaces between chains.
- d–C · 5193 Ų buried · 36 hydrogen bonds · protein-protein
- d–D · 3482 Ų buried · 23 hydrogen bonds · protein-protein
- c–C · 3478 Ų buried · 18 hydrogen bonds · protein-protein
- D–C · 3377 Ų buried · 10 hydrogen bonds · protein-protein
- A–d · 2618 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 7UM0 · Structure of the phage AR9 non-virion RNA polymerase holoenzyme in complex with two DNA… · 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 A0A172JIC8
- Every structure of UniProt A0A172JIH0
- Every structure of UniProt A0A172JI16
- Every structure of UniProt A0A172JI62
- Every structure of UniProt A0A172JHZ2
- Elsewhere: RCSB PDB 7UM0 · PDBe 7UM0 · UniProt A0A172JIC8 · UniProt A0A172JIH0 · UniProt A0A172JI16 · UniProt A0A172JI62 · UniProt A0A172JHZ2
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