Research workbench
X-ray crystal structure of the transcription initiation complex of the N4 mini-vrnap with P2 promoter: mismatch complex
Analyse X-ray crystal structure of the transcription initiation complex of the N4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3Q0A
- Type
- protein + DNA
- Length
- 2,229 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*A*GP*TP*CP*AP*AP*AP…
- UniProt
- Q859P9
- Ligands
- GTP, PO4
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 56% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Virion RNA polymerase | protein | 1095 | 56% helix, 11% strand | Q859P9 |
| C, D | DNA (5'- D(*TP*GP*CP*CP*TP*CP*CP*CP*AP*GP*GP*CP*A*GP*TP*CP*AP*AP*AP*AP*GP*AP*A P*GP*CP*GP*GP*AP*GP*CP*TP*TP*CP*TP*TP*C)-3') | dna | 20 | — | — |
| B | Virion RNA polymerase | protein | 1094 | 57% helix, 11% strand | Q859P9 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, C, B, D
- PO4 · Phosphate 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1029 | 0.86 | 0.88 | 103 | empty |
| 2 | 819 | 0.85 | 0.88 | 89 | empty |
| 3 | 1066 | 0.77 | 0.79 | 84 | empty |
| 4 | 301 | 0.72 | 0.85 | 33 | empty |
| 5 | 916 | 0.71 | 0.76 | 97 | empty |
Interfaces
3 interfaces between chains.
- B–D · 2051 Ų buried · 33 hydrogen bonds · protein-nucleic
- A–C · 2041 Ų buried · 36 hydrogen bonds · protein-nucleic
- A–B · 1133 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 3Q0A · X-ray crystal structure of the transcription initiation complex of the N4 mini-vRNAP with… · 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 3Q0A · PDBe 3Q0A · UniProt Q859P9
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