Research workbench
Structure of bacteriophage T7 lagging-strand DNA polymerase (D5A/E7A) interacting with primase domains of two GP4 subunits bound to an RNA/DNA hybrid and dttp (from LAGS1)
Analyse Structure of bacteriophage T7 lagging-strand DNA polymerase (D5A/E7A)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6N9U
- Type
- protein + DNA + RNA
- Length
- 1,081 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA PRIMASE/HELICASE; DNA-directed DNA polymerase; RNA…
- EC
- 2.7.7.-, 3.6.4.12, 2.7.7.7, 3.1.11.-
- UniProt
- P03692, P00581
- Ligands
- TTP, MG, ZN
- Pockets
- 15 · best druggability 0.82
Structure
electron microscopy · 5 distinct chains · 30% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | DNA PRIMASE/HELICASE (EC 2.7.7.-, 3.6.4.12) | protein | 222 | 18% helix, 24% strand | P03692 |
| F | DNA PRIMASE/HELICASE (EC 2.7.7.-, 3.6.4.12) | protein | 196 | 20% helix, 20% strand | P03692 |
| H | DNA-directed DNA polymerase (EC 2.7.7.7, 3.1.11.-) | protein | 645 | 37% helix, 13% strand | P00581 |
| P | RNA (5'-R(*AP*CP*CP*AP*G)-D(P*(DOC))-3') | rna | 6 | — | — |
| T | DNA (44-mer) | dna | 12 | — | — |
Ligands and binding sites
- TTP · Thymidine-5'-triphosphate · ligand · chains H, P, T
- MG · Magnesium ion · metal · 2 copies · chains H
- ZN · Zinc ion · metal · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1071 | 0.82 | 0.84 | 91 | empty |
| 2 | 684 | 0.75 | 0.81 | 64 | TTP, MG |
| 3 | 752 | 0.74 | 0.79 | 74 | MG |
| 4 | 584 | 0.69 | 0.79 | 51 | empty |
| 5 | 115 | 0.59 | 0.85 | 17 | empty |
Interfaces
7 interfaces between chains.
- E–H · 1080 Ų buried · 10 hydrogen bonds · protein-protein
- H–T · 997 Ų buried · 10 hydrogen bonds · protein-nucleic
- H–P · 577 Ų buried · 9 hydrogen bonds · protein-nucleic
- F–H · 539 Ų buried · 4 hydrogen bonds · protein-protein
- E–T · 390 Ų buried · 0 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 disulfide, 1 modified (disulfide, nucleotide modification).
Compared structures
- 6N9U · Structure of bacteriophage T7 lagging-strand DNA polymerase (D5A/E7A) interacting with… · the same entry in another collection · chain E against E, 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 6N9U · PDBe 6N9U · UniProt P03692 · UniProt P00581
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