Research workbench
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 (LagS2)
Analyse Structure of bacteriophage T7 lagging-strand DNA polymerase (D5A/E7A) and gp4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6N9W
- Type
- protein + DNA + RNA
- Length
- 2,440 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 4.0
- 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 4.0 · 9 distinct chains · 32% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA primase/helicase (EC 2.7.7.-, 3.6.4.12) | protein | 496 | 28% helix, 21% strand | P03692 |
| B | DNA primase/helicase (EC 2.7.7.-, 3.6.4.12) | protein | 474 | 30% helix, 20% strand | P03692 |
| C | DNA primase/helicase (EC 2.7.7.-, 3.6.4.12) | protein | 276 | 35% helix, 19% strand | P03692 |
| D | DNA primase/helicase (EC 2.7.7.-, 3.6.4.12) | protein | 261 | 29% helix, 20% strand | P03692 |
| E | DNA primase/helicase (EC 2.7.7.-, 3.6.4.12) | protein | 241 | 28% helix, 17% strand | P03692 |
| F | DNA primase/helicase (EC 2.7.7.-, 3.6.4.12) | protein | 17 | 47% helix, 6% strand | P03692 |
| H | DNA-directed DNA polymerase (EC 2.7.7.7, 3.1.11.-) | protein | 645 | 39% helix, 12% strand | P00581 |
| P | Primer | rna | 6 | — | — |
| T | Template | dna | 24 | — | — |
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 A
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 | 696 | 0.82 | 0.86 | 75 | TTP, MG |
| 2 | 1062 | 0.82 | 0.83 | 92 | empty |
| 3 | 664 | 0.81 | 0.86 | 78 | TTP, MG |
| 4 | 630 | 0.81 | 0.86 | 79 | TTP, MG |
| 5 | 501 | 0.80 | 0.87 | 70 | TTP, MG |
Interfaces
16 interfaces between chains.
- A–B · 2304 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 2271 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1975 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 1512 Ų buried · 10 hydrogen bonds · protein-protein
- A–H · 1014 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide, 1 modified (disulfide, nucleotide modification).
Compared structures
- 6N9W · 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 6N9W · PDBe 6N9W · UniProt P03692 · UniProt P00581
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