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 (LAGS1)
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
- 6N9V
- Type
- protein + DNA + RNA
- Length
- 2,684 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- 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 0.81
Structure
electron microscopy · 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 | 253 | 30% helix, 20% strand | P03692 |
| B | DNA PRIMASE/HELICASE (EC 2.7.7.-, 3.6.4.12) | protein | 275 | 31% helix, 19% strand | P03692 |
| C | DNA PRIMASE/HELICASE (EC 2.7.7.-, 3.6.4.12) | protein | 272 | 31% helix, 20% strand | P03692 |
| D | DNA PRIMASE/HELICASE (EC 2.7.7.-, 3.6.4.12) | protein | 267 | 30% helix, 19% strand | P03692 |
| E | DNA PRIMASE/HELICASE (EC 2.7.7.-, 3.6.4.12) | protein | 483 | 23% helix, 23% strand | P03692 |
| F | DNA PRIMASE/HELICASE (EC 2.7.7.-, 3.6.4.12) | protein | 456 | 26% helix, 19% 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 | 27 | — | — |
Ligands and binding sites
- TTP · Thymidine-5'-triphosphate · ligand · 6 copies · chains A, B, C, D, E, F, H, P, T
- MG · Magnesium ion · metal · 7 copies · chains B, C, D, E, F, H
- ZN · Zinc ion · metal · chains 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1030 | 0.81 | 0.83 | 93 | empty |
| 2 | 580 | 0.81 | 0.87 | 75 | TTP, MG |
| 3 | 646 | 0.81 | 0.86 | 72 | TTP, MG |
| 4 | 553 | 0.81 | 0.87 | 69 | TTP, MG |
| 5 | 354 | 0.80 | 0.90 | 50 | TTP, MG |
Interfaces
18 interfaces between chains.
- A–B · 2108 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 2067 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 2029 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 1989 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 1913 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide, 1 modified (disulfide, nucleotide modification).
Compared structures
- 6N9V · 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 6N9V · PDBe 6N9V · UniProt P03692 · UniProt P00581
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