MolNFT v1 · #75830 · protein + DNA
X-ray crystal structure of the N4 mini-vrnap and P2_7A promoter transcription initiation complex with pppgpg and pyrophosphate: product complex
3Q24 · Virion RNA polymerase: “X-ray crystal structure of the N4 mini-vrnap and P2_7A promoter transcription initiation complex with pppgpg…”. X-ray diffraction, 4 ligands (POP, GTP, G), 20 pockets (best druggability 0.86). MolNFT v1…
- PDB
- 3Q24
- Type
- protein + DNA
- Length
- 2,232 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Virion RNA polymerase; DNA (5'- D(*TP*GP*CP*CP*TP*CP*CP*CP*AP*GP*GP*CP*AP*TP*CP*CP*AP*AP*A…
- EC
- 2.7.7.6
- UniProt
- Q859P9
- Ligands
- POP, GTP, G, 2HP
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 57% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Virion RNA polymerase (EC 2.7.7.6) | protein | 1095 | 57% helix, 11% strand | Q859P9 |
| B | Virion RNA polymerase (EC 2.7.7.6) | protein | 1094 | 57% helix, 11% strand | Q859P9 |
| C | DNA (5'- D(*TP*GP*CP*CP*TP*CP*CP*CP*AP*GP*GP*CP*AP*TP*CP*CP*AP*AP*AP*AP*GP*AP* AP*GP*CP*GP*GP*AP*GP*CP*TP*TP*CP*TP*TP*C)-3') | dna | 21 | — | — |
| D | DNA (5'- D(*TP*GP*CP*CP*TP*CP*CP*CP*AP*GP*GP*CP*AP*TP*CP*CP*AP*AP*AP*AP*GP*AP* AP*GP*CP*GP*GP*AP*GP*CP*TP*TP*CP*TP*TP*C)-3') | dna | 22 | — | — |
Ligands and binding sites
- POP · Pyrophosphate 2- · ligand · 2 copies · chains A, B
- GTP · Guanosine-5'-triphosphate · ligand · chains A, C
- G · Guanosine-5'-monophosphate · ligand · chains A, C
- 2HP · Dihydrogenphosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 998 | 0.86 | 0.87 | 112 | empty |
| 2 | 1001 | 0.85 | 0.86 | 104 | empty |
| 3 | 437 | 0.71 | 0.82 | 45 | empty |
| 4 | 456 | 0.71 | 0.81 | 37 | empty |
| 5 | 579 | 0.69 | 0.79 | 73 | empty |
Interfaces
4 interfaces between chains.
- B–D · 2047 Ų buried · 32 hydrogen bonds · protein-nucleic
- A–C · 1971 Ų buried · 31 hydrogen bonds · protein-nucleic
- A–B · 950 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 33 Ų buried · 0 hydrogen bonds · protein-nucleic
Compared structures
- 3Q24 · X-ray crystal structure of the N4 mini-VRNAP and P2_7a promoter transcription initiation… · 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 Q859P9
- Elsewhere: RCSB PDB 3Q24 · PDBe 3Q24 · UniProt Q859P9
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