MolNFT v1 · #21775 · protein + DNA
Ternary 5' complex of T7 DNA polymerase with a DNA PRIMER/TEMPLATE containing a cis-syn thymine dimer on the template and an incoming nucleotide
1SL2 · 5'- D(*CP*GP*AP*AP*AP*AP*CP*GP*AP*CP*GP*GP*CP*CP*AP*GP*TP*GP…: “Ternary 5' complex of T7 DNA polymerase with a DNA PRIMER/TEMPLATE containing a cis-syn thymine dimer on the…”. X-ray diffraction, 2 ligands (DAD, MG), 6 pockets (best…
- PDB
- 1SL2
- Type
- protein + DNA
- Length
- 791 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'- D(*CP*GP*AP*AP*AP*AP*CP*GP*AP*CP*GP*GP*CP*CP*AP*GP*TP*GP*CP *CP*TP*(2DA))-3'…
- EC
- 2.7.7.7
- UniProt
- P00581, P0AA25
- Ligands
- DAD, MG
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P | 5'- D(*CP*GP*AP*AP*AP*AP*CP*GP*AP*CP*GP*GP*CP*CP*AP*GP*TP*GP*CP *CP*TP*(2DA))-3' | dna | 9 | — | — |
| T | 5'-D(*CP*CP*CP*(TTD) P*AP*GP*GP*CP*AP*CP*TP*GP*GP*CP*CP*GP*TP*CP*GP*TP*TP*TP*TP* CP*G)-3' | dna | 10 | — | — |
| A | DNA polymerase (EC 2.7.7.7) | protein | 667 | 49% helix, 14% strand | P00581 |
| B | Thioredoxin 1 | protein | 105 | 35% helix, 29% strand | P0AA25 |
Ligands and binding sites
- DAD · 2',3'-dideoxyadenosine-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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 751 | 0.75 | 0.79 | 62 | MG |
| 2 | 782 | 0.75 | 0.79 | 89 | MG, DAD |
| 3 | 61 | 0.70 | 0.96 | 18 | empty |
| 4 | 301 | 0.67 | 0.83 | 30 | empty |
| 5 | 265 | 0.57 | 0.78 | 33 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1082 Ų buried · 11 hydrogen bonds · protein-protein
- T–A · 989 Ų buried · 23 hydrogen bonds · protein-nucleic
- P–A · 648 Ų buried · 9 hydrogen bonds · protein-nucleic
- P–T · 439 Ų buried · 41 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 1SL2 · Ternary 5' complex of T7 DNA polymerase with a DNA primer/template containing a cis-syn… · the same entry in another collection · chain P against P, TM-score 1.00
- P0AA25 · AlphaFold monomer V2.0 prediction for thioredoxin 1 (P0AA25) · 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 P0AA25
- Elsewhere: RCSB PDB 1SL2 · PDBe 1SL2 · UniProt P00581 · UniProt P0AA25
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