Research workbench
Structure of bacteriophage T7 E343Q mutant GP4 helicase-primase in complex with ssdna, dttp, ac dinucleotide and CTP (form II)
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
- 6N7S
- Type
- protein + DNA
- Length
- 1,620 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 0.81
Structure
electron microscopy · 7 distinct chains · 26% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA PRIMASE/HELICASE (EC 2.7.7.-, 3.6.4.12) | protein | 271 | 28% helix, 17% strand | P03692 |
| B | DNA PRIMASE/HELICASE (EC 2.7.7.-, 3.6.4.12) | protein | 273 | 26% helix, 18% strand | P03692 |
| C | DNA PRIMASE/HELICASE (EC 2.7.7.-, 3.6.4.12) | protein | 275 | 24% helix, 17% strand | P03692 |
| D | DNA PRIMASE/HELICASE (EC 2.7.7.-, 3.6.4.12) | protein | 271 | 24% helix, 13% strand | P03692 |
| E | DNA PRIMASE/HELICASE (EC 2.7.7.-, 3.6.4.12) | protein | 259 | 26% helix, 14% strand | P03692 |
| F | DNA PRIMASE/HELICASE (EC 2.7.7.-, 3.6.4.12) | protein | 258 | 24% helix, 18% strand | P03692 |
| T | DNA (25-mer) | dna | 13 | — | — |
Ligands and binding sites
- TTP · Thymidine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D, E
- MG · Magnesium ion · metal · 4 copies · chains 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 796 | 0.81 | 0.84 | 95 | TTP, MG |
| 2 | 541 | 0.80 | 0.87 | 68 | TTP, MG |
| 3 | 1002 | 0.80 | 0.81 | 90 | empty |
| 4 | 769 | 0.80 | 0.84 | 83 | TTP, MG |
| 5 | 464 | 0.79 | 0.87 | 65 | TTP, MG |
Interfaces
12 interfaces between chains.
- B–C · 2174 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 2039 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 1963 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 1915 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 1440 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6N7S · 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 6N7S · PDBe 6N7S · UniProt P03692
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