MolNFT v2 · #158857 · protein + DNA + RNA
Structure of bacteriophage T7 lagging-strand DNA polymerase (D5A/E7A) and gp4 (helicase/primase) bound to DNA including RNA/DNA hybrid, and an incoming dTTP (LagS3)
6N9X · DNA primase/helicase: “Structure of bacteriophage T7 lagging-strand DNA polymerase (D5A/E7A) and gp4 (helicase/primase) bound to DNA…”. Electron microscopy at 4.1, 3 ligands (TTP, MG, ZN), 20 pockets (best druggability 0.82). MolNFT…
- PDB
- 6N9X
- Type
- protein + DNA + RNA
- Length
- 2,450 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 4.1
- Source
- Enterobacteria phage T7; SYNTHETIC CONSTRUCT
- Molecule
- DNA primase/helicase; DNA-directed DNA polymerase; Primer; Template
- EC
- 2.7.7.-, 3.6.4.12, 2.7.7.7, 3.1.11.-
- UniProt
- P03692, P00581
- Ligands
- TTP, MG, ZN
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · resolution 4.1 · 9 distinct chains · 30% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA primase/helicase (EC 2.7.7.-, 3.6.4.12) | protein | 271 | 29% helix, 18% strand | P03692 |
| B | DNA primase/helicase (EC 2.7.7.-, 3.6.4.12) | protein | 500 | 25% helix, 21% strand | P03692 |
| C | DNA primase/helicase (EC 2.7.7.-, 3.6.4.12) | protein | 474 | 28% helix, 19% strand | P03692 |
| D | DNA primase/helicase (EC 2.7.7.-, 3.6.4.12) | protein | 271 | 30% helix, 20% strand | P03692 |
| E | DNA primase/helicase (EC 2.7.7.-, 3.6.4.12) | protein | 241 | 30% helix, 20% strand | P03692 |
| F | DNA primase/helicase (EC 2.7.7.-, 3.6.4.12) | protein | 17 | 29% helix, 12% strand | P03692 |
| H | DNA-directed DNA polymerase (EC 2.7.7.7, 3.1.11.-) | protein | 645 | 37% helix, 13% strand | P00581 |
| P | Primer | rna | 6 | — | — |
| T | Template | dna | 25 | — | — |
Ligands and binding sites
- TTP · Thymidine-5'-triphosphate · ligand · 5 copies · chains A, B, C, D, E, H, P, T
- MG · Magnesium ion · metal · 6 copies · chains B, C, D, E, H
- ZN · Zinc ion · metal · chains 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 596 | 0.82 | 0.87 | 81 | TTP, MG |
| 2 | 699 | 0.82 | 0.86 | 83 | TTP, MG |
| 3 | 621 | 0.81 | 0.87 | 74 | TTP, MG |
| 4 | 613 | 0.81 | 0.86 | 71 | TTP, MG |
| 5 | 714 | 0.81 | 0.85 | 68 | empty |
Interfaces
16 interfaces between chains.
- B–C · 2265 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 2114 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 2092 Ų buried · 15 hydrogen bonds · protein-protein
- D–E · 1942 Ų buried · 12 hydrogen bonds · protein-protein
- H–T · 1006 Ų buried · 13 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 disulfide, 1 modified (disulfide, nucleotide modification).
Compared structures
- 6N9X · Structure of bacteriophage T7 lagging-strand DNA polymerase (D5A/E7A) and GP4… · 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
- Every structure of UniProt P00581
- Elsewhere: RCSB PDB 6N9X · PDBe 6N9X · UniProt P03692 · UniProt P00581
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