MolNFT v1 · #22522 · protein + DNA
T7 DNA polymerase complexed to DNA PRIMER/TEMPLATE,A nucleoside triphosphate, and its processivity factor thioredoxin
1T7P · DNA (5'-D(P*GP*CP*CP*AP*GP*TP*GP*CP*CP*AP*2DA)-3'): “T7 DNA polymerase complexed to DNA PRIMER/TEMPLATE,A nucleoside triphosphate, and its processivity factor…”. X-ray diffraction, 2 ligands (DG3, MG), 6 pockets (best druggability…
- PDB
- 1T7P
- Type
- protein + DNA
- Length
- 791 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(P*GP*CP*CP*AP*GP*TP*GP*CP*CP*AP*2DA)-3'); DNA…
- EC
- 2.7.7.7, 3.1.11.-
- UniProt
- P00581, P0AA27
- Ligands
- DG3, MG
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P | DNA (5'-D(P*GP*CP*CP*AP*GP*TP*GP*CP*CP*AP*2DA)-3') | dna | 11 | — | — |
| T | DNA (5'-D(P*CP*CP*TP*TP*GP*GP*CP*AP*CP*TP*GP*GP*C)-3') | dna | 13 | — | — |
| A | DNA-directed DNA polymerase (EC 2.7.7.7, 3.1.11.-) | protein | 662 | 49% helix, 14% strand | P00581 |
| B | Thioredoxin 1 | protein | 105 | 36% helix, 30% strand | P0AA27 |
Ligands and binding sites
- DG3 · 2'-3'-dideoxyguanosine-5'-triphosphate · ligand · chains P, T, A
- MG · Magnesium ion · metal · 3 copies · chains A, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 759 | 0.75 | 0.80 | 70 | MG |
| 2 | 517 | 0.72 | 0.81 | 51 | empty |
| 3 | 746 | 0.72 | 0.78 | 61 | DG3, MG |
| 4 | 300 | 0.70 | 0.85 | 34 | empty |
| 5 | 125 | 0.43 | 0.76 | 22 | empty |
Interfaces
4 interfaces between chains.
- T–A · 1171 Ų buried · 25 hydrogen bonds · protein-nucleic
- A–B · 971 Ų buried · 10 hydrogen bonds · protein-protein
- P–A · 770 Ų buried · 14 hydrogen bonds · protein-nucleic
- P–T · 503 Ų buried · 39 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 1T7P · T7 DNA polymerase complexed to DNA PRIMER/TEMPLATE,A nucleoside triphosphate, and its… · the same entry in another collection · chain P against P, TM-score 1.00
- P0AA27 · AlphaFold monomer V2.0 prediction for thioredoxin 1 (P0AA27) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P0AA27
- Elsewhere: RCSB PDB 1T7P · PDBe 1T7P · UniProt P00581 · UniProt P0AA27
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