Research workbench
T7 DNA polymerase ternary complex with dctp at the insertion site.
Analyse T7 DNA polymerase ternary complex with dctp at the insertion site. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1T8E
- Type
- protein + DNA
- Length
- 851 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'- D(P*CP*GP*AP*AP*AP*AP*CP*GP*AP*CP*GP*GP*CP*CP*AP*GP*TP*GP*C P*CP*AP*(2DT))-3'…
- EC
- 2.7.7.7
- UniProt
- P00581, P0AA25
- Ligands
- DCT, MG, SO4
- Pockets
- 10 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 5'- D(P*CP*GP*AP*AP*AP*AP*CP*GP*AP*CP*GP*GP*CP*CP*AP*GP*TP*GP*C P*CP*AP*(2DT))-3' | dna | 22 | — | — |
| D | 25-mer | dna | 25 | — | — |
| A | DNA polymerase (EC 2.7.7.7) | protein | 698 | 46% helix, 14% strand | P00581 |
| B | Thioredoxin 1 | protein | 106 | 36% helix, 27% strand | P0AA25 |
Ligands and binding sites
- DCT · 2',3'-dideoxycytidine 5'-triphosphate · ligand · chains C, D, A
- MG · Magnesium ion · metal · 3 copies · chains A, C
- SO4 · Sulfate ion · ion · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A
- PG4 · Tetraethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 709 | 0.73 | 0.79 | 70 | MG, SO4, PG4 |
| 2 | 764 | 0.72 | 0.78 | 60 | MG, DCT |
| 3 | 598 | 0.71 | 0.79 | 49 | empty |
| 4 | 312 | 0.69 | 0.84 | 30 | empty |
| 5 | 241 | 0.56 | 0.79 | 22 | empty |
Interfaces
5 interfaces between chains.
- D–A · 1485 Ų buried · 27 hydrogen bonds · protein-nucleic
- A–B · 1085 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 970 Ų buried · 78 hydrogen bonds · nucleic-nucleic
- C–A · 968 Ų buried · 19 hydrogen bonds · protein-nucleic
- C–B · 69 Ų buried · 3 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
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 P00581
- Every structure of UniProt P0AA25
- Elsewhere: RCSB PDB 1T8E · PDBe 1T8E · UniProt P00581 · UniProt P0AA25
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