MolNFT v1 · #75829 · protein + DNA
X-ray crystal structure of the N4 mini-vrnap and P2_7A promoter transcription initiation complex with gmpcpp and manganese: sustrate complex II
3Q23 · Virion RNA polymerase: “X-ray crystal structure of the N4 mini-vrnap and P2_7A promoter transcription initiation complex with gmpcpp…”. X-ray diffraction, 3 ligands (G2P, MN, 2HP), 20 pockets (best druggability 0.86). MolNFT v1…
- PDB
- 3Q23
- 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*AP*TP*CP*CP*AP*AP*A…
- EC
- 2.7.7.6
- UniProt
- Q859P9
- Ligands
- G2P, MN, 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 |
| 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 | 19 | — | — |
| B | Virion RNA polymerase (EC 2.7.7.6) | protein | 1094 | 57% helix, 11% strand | Q859P9 |
| 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 | 21 | — | — |
Ligands and binding sites
- G2P · Phosphomethylphosphonic acid guanylate ester · ligand · 4 copies · chains A, C, B, D
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
- 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 | 1009 | 0.86 | 0.87 | 94 | empty |
| 2 | 911 | 0.85 | 0.87 | 98 | empty |
| 3 | 526 | 0.72 | 0.81 | 46 | empty |
| 4 | 900 | 0.71 | 0.76 | 61 | empty |
| 5 | 272 | 0.71 | 0.86 | 37 | empty |
Interfaces
4 interfaces between chains.
- B–D · 2010 Ų buried · 33 hydrogen bonds · protein-nucleic
- A–C · 1840 Ų buried · 30 hydrogen bonds · protein-nucleic
- A–B · 996 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 44 Ų buried · 1 hydrogen bond · protein-nucleic
Compared structures
- 3Q23 · 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 3Q23 · PDBe 3Q23 · UniProt Q859P9
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