Research workbench
Binary 3' complex of T7 DNA polymerase with a DNA PRIMER/TEMPLATE containing a disordered cis-syn thymine dimer on the template
Analyse Binary 3' complex of T7 DNA polymerase with a DNA PRIMER/TEMPLATE containing a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1SKW
- Type
- protein + DNA
- Length
- 801 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*C*GP*GP*CP*CP*AP*GP*TP*GP*CP* CP*(2DT))-3'…
- EC
- 2.7.7.7
- UniProt
- P00581, P0AA25
- Ligands
- MG
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P | 5'- D(*CP*GP*AP*AP*AP*AP*CP*GP*AP*C*GP*GP*CP*CP*AP*GP*TP*GP*CP* CP*(2DT))-3' | dna | 8 | — | — |
| 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 | 678 | 48% helix, 14% strand | P00581 |
| B | Thioredoxin 1 | protein | 105 | 35% helix, 30% strand | P0AA25 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 760 | 0.75 | 0.80 | 70 | MG |
| 2 | 64 | 0.71 | 0.97 | 16 | empty |
| 3 | 249 | 0.67 | 0.84 | 31 | empty |
| 4 | 327 | 0.61 | 0.78 | 40 | empty |
| 5 | 152 | 0.50 | 0.78 | 28 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1068 Ų buried · 8 hydrogen bonds · protein-protein
- T–A · 913 Ų buried · 16 hydrogen bonds · protein-nucleic
- P–A · 676 Ų buried · 11 hydrogen bonds · protein-nucleic
- P–T · 390 Ų buried · 33 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 1SKW · Binary 3' complex of T7 DNA polymerase with a DNA primer/template containing a disordered… · 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 1SKW · PDBe 1SKW · UniProt P00581 · UniProt P0AA25
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