MolNFT v1 · #27112 · protein + DNA
T7 DNA polymerase in complex with a PRIMER/TEMPLATE DNA containing a disordered N-2 aminofluorene on the template, crystallized with dideoxy-ATP as the incoming nucleotide.
1X9W · 5'- D(*GP*GP*AP*GP*AP*GP*TP*GP*AP*TP*T*GP*GP*T*AP*GP*TP*GP*T…: “T7 DNA polymerase in complex with a PRIMER/TEMPLATE DNA containing a disordered N-2 aminofluorene on the…”. X-ray diffraction, 1 ligand (MG), 7 pockets (best…
- PDB
- 1X9W
- Type
- protein + DNA
- Length
- 800 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'- D(*GP*GP*AP*GP*AP*GP*TP*GP*AP*TP*T*GP*GP*T*AP*GP*TP*GP*TP*G P*AP*(2DT))-3'…
- EC
- 2.7.7.7
- UniProt
- P00581, P0AA25
- Ligands
- MG
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 5'- D(*GP*GP*AP*GP*AP*GP*TP*GP*AP*TP*T*GP*GP*T*AP*GP*TP*GP*TP*G P*AP*(2DT))-3' | dna | 11 | — | — |
| D | 5'-D(*CP*CP*CP*(AFG) *AP*TP*CP*AP*CP*AP*CP*TP*AP*CP*CP*AP*AP*TP*CP*AP*CP*TP*CP*T P*CP*C)-3' | dna | 11 | — | — |
| A | DNA polymerase (EC 2.7.7.7) | protein | 673 | 47% helix, 14% strand | P00581 |
| B | Thioredoxin 1 | protein | 105 | 35% helix, 29% 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
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 785 | 0.74 | 0.79 | 69 | MG |
| 2 | 57 | 0.70 | 0.97 | 17 | empty |
| 3 | 295 | 0.68 | 0.83 | 31 | empty |
| 4 | 504 | 0.64 | 0.77 | 40 | empty |
| 5 | 245 | 0.57 | 0.78 | 31 | empty |
Interfaces
4 interfaces between chains.
- A–B · 969 Ų buried · 7 hydrogen bonds · protein-protein
- D–A · 897 Ų buried · 21 hydrogen bonds · protein-nucleic
- C–A · 780 Ų buried · 12 hydrogen bonds · protein-nucleic
- C–D · 489 Ų buried · 37 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 1X9W · T7 DNA polymerase in complex with a primer/template DNA containing a disordered N-2… · the same entry in another collection · chain C against C, 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 1X9W · PDBe 1X9W · UniProt P00581 · UniProt P0AA25
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