Research workbench
T7 DNA polymerase in complex with an N-2- acetylaminofluorene-adducted DNA
Analyse T7 DNA polymerase in complex with an N-2- acetylaminofluorene-adducted DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1X9M
- Type
- protein + DNA
- Length
- 802 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*TP*GP*GP*TP*AP*GP*TP*GP*TP *GP*AP*(2DT))-3'…
- EC
- 2.7.7.7
- UniProt
- P00581, P0AA25
- Ligands
- MG
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 5'- D(*GP*GP*AP*GP*AP*GP*TP*GP*AP*TP*TP*GP*GP*TP*AP*GP*TP*GP*TP *GP*AP*(2DT))-3' | dna | 10 | — | — |
| D | 5'-D(*CP*CP*CP*(8FG) P*AP*TP*CP*AP*CP*AP*CP*TP*AP*CP*CP*AP*AP*TP*CP*AP*CP*TP*CP* TP*CP*C)-3' | dna | 12 | — | — |
| A | DNA polymerase (EC 2.7.7.7) | protein | 675 | 48% helix, 14% strand | P00581 |
| B | Thioredoxin 1 | protein | 105 | 39% helix, 28% 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1160 | 0.76 | 0.79 | 93 | MG |
| 2 | 90 | 0.74 | 0.96 | 20 | empty |
| 3 | 314 | 0.70 | 0.84 | 29 | empty |
| 4 | 60 | 0.69 | 0.96 | 16 | empty |
| 5 | 304 | 0.50 | 0.73 | 35 | empty |
Interfaces
4 interfaces between chains.
- D–A · 1321 Ų buried · 28 hydrogen bonds · protein-nucleic
- A–B · 1105 Ų buried · 11 hydrogen bonds · protein-protein
- C–A · 804 Ų buried · 11 hydrogen bonds · protein-nucleic
- C–D · 474 Ų buried · 33 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 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 1X9M · PDBe 1X9M · UniProt P00581 · UniProt P0AA25
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