MolNFT v1 · #187067 · protein + DNA
X-ray structure of the phage AR9 non-virion RNA polymerase holoenzyme in complex with a forked oligonucleotide containing the P077 promoter
7S01 · DNA-directed RNA polymerase subunit: “X-ray structure of the phage AR9 non-virion RNA polymerase holoenzyme in complex with a forked…”. X-ray diffraction, 5 ligands (UMP, DG, DT), 20 pockets (best druggability 0.85). MolNFT v1…
- PDB
- 7S01
- Type
- protein + DNA
- Length
- 2,723 residues
- Chains
- 9
- Method
- x-ray diffraction
- 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
- UMP, DG, DT, DA, ZN
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 9 distinct chains · 44% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-directed RNA polymerase subunit | protein | 463 | 65% helix, 5% strand | A0A172JIC8 |
| d | DNA-directed RNA polymerase beta' subunit | protein | 426 | 40% helix, 18% strand | A0A172JIH0 |
| c | DNA-directed RNA polymerase beta subunit | protein | 484 | 39% helix, 22% strand | A0A172JI16 |
| D | DNA-directed RNA polymerase (EC 2.7.7.6) | protein | 631 | 46% helix, 15% strand | A0A172JI62 |
| C | DNA-directed RNA polymerase (EC 2.7.7.6) | protein | 649 | 32% helix, 25% strand | A0A172JHZ2 |
| N | Non-template strand of the forked DNA oligonucleotide (downstream copy) | dna | 13 | — | — |
| T | Template strand of the forked DNA oligonucleotide (downstream copy) containing the P077 AR9 promoter motif | dna | 21 | — | — |
| t | Non-template strand of the forked DNA oligonucleotide (downstream copy) | dna | 14 | — | — |
| n | Template strand of the forked DNA oligonucleotide (downstream copy) containing the P077 AR9 promoter motif | dna | 22 | — | — |
Ligands and binding sites
- UMP · 2'-deoxyuridine 5'-monophosphate · ligand · 5 copies · chains A, d, t, c, C, T
- DG · 2'-deoxyguanosine-5'-monophosphate · ligand · chains A, c
- DT · Thymidine-5'-monophosphate · ligand · chains t, n
- DA · 2'-deoxyadenosine-5'-monophosphate · ligand · chains A, n
- 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 | 574 | 0.85 | 0.90 | 62 | empty |
| 2 | 941 | 0.76 | 0.79 | 76 | empty |
| 3 | 232 | 0.76 | 0.90 | 30 | empty |
| 4 | 252 | 0.75 | 0.89 | 51 | empty |
| 5 | 686 | 0.75 | 0.81 | 55 | empty |
Interfaces
22 interfaces between chains.
- d–C · 5320 Ų buried · 49 hydrogen bonds · protein-protein
- c–C · 3611 Ų buried · 39 hydrogen bonds · protein-protein
- D–C · 3585 Ų buried · 38 hydrogen bonds · protein-protein
- d–D · 3373 Ų buried · 32 hydrogen bonds · protein-protein
- A–d · 2668 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 7S01 · X-ray structure of the phage AR9 non-virion RNA polymerase holoenzyme in complex with a… · 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 7S01 · PDBe 7S01 · UniProt A0A172JIC8 · UniProt A0A172JIH0 · UniProt A0A172JI16 · UniProt A0A172JI62 · UniProt A0A172JHZ2
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