Research workbench
Structure of bacteriophage T7 gp4 (helicase-primase, E343Q mutant) in complex with ssDNA, dTTP, AC dinucleotide, and CTP (from multiple lead complexes)
Analyse Structure of bacteriophage T7 gp4 (helicase-primase, E343Q mutant) in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6N7V
- Type
- protein + DNA
- Length
- 1,622 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.8
- Source
- Enterobacteria phage T7; SYNTHETIC CONSTRUCT
- Molecule
- DNA primase/helicase; DNA (93-mer)
- EC
- 2.7.7.-, 3.6.4.12
- UniProt
- P03692
- Ligands
- TTP, MG
- Pockets
- 19 · best druggability 0.82
Structure
electron microscopy · resolution 3.8 · 7 distinct chains · 31% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA primase/helicase (EC 2.7.7.-, 3.6.4.12) | protein | 271 | 33% helix, 19% strand | P03692 |
| B | DNA primase/helicase (EC 2.7.7.-, 3.6.4.12) | protein | 274 | 31% helix, 20% strand | P03692 |
| C | DNA primase/helicase (EC 2.7.7.-, 3.6.4.12) | protein | 276 | 34% helix, 21% strand | P03692 |
| D | DNA primase/helicase (EC 2.7.7.-, 3.6.4.12) | protein | 271 | 31% helix, 19% strand | P03692 |
| E | DNA primase/helicase (EC 2.7.7.-, 3.6.4.12) | protein | 259 | 29% helix, 20% strand | P03692 |
| F | DNA primase/helicase (EC 2.7.7.-, 3.6.4.12) | protein | 255 | 27% helix, 22% strand | P03692 |
| T | DNA (93-mer) | dna | 16 | — | — |
Ligands and binding sites
- TTP · Thymidine-5'-triphosphate · ligand · 5 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 5 copies · chains B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 575 | 0.82 | 0.87 | 74 | TTP, MG |
| 2 | 727 | 0.81 | 0.85 | 85 | TTP, MG |
| 3 | 705 | 0.81 | 0.85 | 82 | TTP |
| 4 | 656 | 0.80 | 0.85 | 78 | TTP, MG |
| 5 | 612 | 0.80 | 0.86 | 89 | TTP, MG |
Interfaces
12 interfaces between chains.
- B–C · 2218 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 2100 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 2086 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 1964 Ų buried · 18 hydrogen bonds · protein-protein
- D–E · 1944 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6N7V · Structure of bacteriophage T7 GP4 (helicase-primase, E343Q mutant) in complex with ssdna… · 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 P03692
- Elsewhere: RCSB PDB 6N7V · PDBe 6N7V · UniProt P03692
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