Research workbench
Structure of bacteriophage T7 E343Q mutant GP4 helicase-primase in complex with ssdna, dttp, ac dinucleotide and CTP (form III)
Analyse Structure of bacteriophage T7 E343Q mutant GP4 helicase-primase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6N7T
- Type
- protein + DNA
- Length
- 1,626 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA PRIMASE/HELICASE; DNA (25-mer)
- EC
- 2.7.7.-, 3.6.4.12
- UniProt
- P03692
- Ligands
- TTP, MG
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 7 distinct chains · 30% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA PRIMASE/HELICASE (EC 2.7.7.-, 3.6.4.12) | protein | 271 | 31% helix, 19% strand | P03692 |
| B | DNA PRIMASE/HELICASE (EC 2.7.7.-, 3.6.4.12) | protein | 274 | 33% helix, 19% strand | P03692 |
| C | DNA PRIMASE/HELICASE (EC 2.7.7.-, 3.6.4.12) | protein | 275 | 32% helix, 18% strand | P03692 |
| D | DNA PRIMASE/HELICASE (EC 2.7.7.-, 3.6.4.12) | protein | 271 | 31% helix, 18% strand | P03692 |
| E | DNA PRIMASE/HELICASE (EC 2.7.7.-, 3.6.4.12) | protein | 258 | 28% helix, 18% strand | P03692 |
| F | DNA PRIMASE/HELICASE (EC 2.7.7.-, 3.6.4.12) | protein | 261 | 26% helix, 20% strand | P03692 |
| T | DNA (25-mer) | dna | 16 | — | — |
Ligands and binding sites
- TTP · Thymidine-5'-triphosphate · ligand · 5 copies · chains A, F, B, C, D, E
- MG · Magnesium ion · metal · 5 copies · chains A, F, B, C, D, E
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 | 359 | 0.82 | 0.91 | 48 | TTP, MG |
| 2 | 648 | 0.81 | 0.86 | 80 | TTP, MG |
| 3 | 336 | 0.81 | 0.91 | 49 | TTP, MG |
| 4 | 590 | 0.81 | 0.86 | 73 | TTP, MG |
| 5 | 558 | 0.80 | 0.86 | 68 | TTP, MG |
Interfaces
12 interfaces between chains.
- B–C · 2145 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 2071 Ų buried · 17 hydrogen bonds · protein-protein
- A–F · 2060 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 2048 Ų buried · 20 hydrogen bonds · protein-protein
- D–E · 1910 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6N7T · Structure of bacteriophage T7 E343Q mutant gp4 helicase-primase 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 6N7T · PDBe 6N7T · UniProt P03692
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.