MolNFT v1 · #59648 · protein + DNA
X-ray crystal structure of the N4 mini-vrnap P2_7A promoter complex soaked with MGCL2
3C46 · Virion RNA polymerase: “X-ray crystal structure of the N4 mini-vrnap P2_7A promoter complex soaked with MGCL2”. X-ray diffraction, 1 ligand (2HP), 20 pockets (best druggability 0.85). MolNFT v1 #59648 on GenesisL1: 3D structure…
- PDB
- 3C46
- 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; P2_7A promoter DNA
- EC
- 2.7.7.6
- UniProt
- Q859P9
- Ligands
- 2HP
- Pockets
- 20 · best druggability 0.85
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 | 56% helix, 11% strand | Q859P9 |
| C | P2_7A promoter DNA | dna | 19 | — | — |
| B | Virion RNA polymerase (EC 2.7.7.6) | protein | 1094 | 57% helix, 11% strand | Q859P9 |
| D | P2_7A promoter DNA | dna | 21 | — | — |
Ligands and binding sites
- 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 928 | 0.85 | 0.87 | 96 | empty |
| 2 | 1133 | 0.84 | 0.85 | 111 | empty |
| 3 | 451 | 0.73 | 0.83 | 50 | empty |
| 4 | 483 | 0.72 | 0.81 | 41 | empty |
| 5 | 556 | 0.69 | 0.79 | 54 | empty |
Interfaces
4 interfaces between chains.
- B–D · 2053 Ų buried · 35 hydrogen bonds · protein-nucleic
- A–C · 1896 Ų buried · 34 hydrogen bonds · protein-nucleic
- A–B · 965 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 40 Ų buried · 1 hydrogen bond · protein-nucleic
Compared structures
- 3C46 · X-ray crystal structure of the N4 mini-vRNAP P2_7a promoter complex soaked with MgCl2 · 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 3C46 · PDBe 3C46 · UniProt Q859P9
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