Research workbench
Y-family DNA polymerase DPO4 in complex with DNA containing abasic lesion
Analyse Y-family DNA polymerase DPO4 in complex with DNA containing abasic lesion in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1N56
- Type
- protein + DNA
- Length
- 744 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*AP*A)-3'; 5'-D(*TP*CP*AP*TP*(3DR)…
- UniProt
- Q97W02
- Ligands
- ATP, MG, CA
- Pockets
- 7 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, E | 5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*CP*TP*AP*A)-3' | dna | 14 | — | — |
| D, F | 5'-D(*TP*CP*AP*TP*(3DR) P*AP*GP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3' | dna | 17 | — | — |
| A, B | DNA polymerase IV | protein | 341 | 44% helix, 25% strand | Q97W02 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains C, D, A, E, F, B
- MG · Magnesium ion · metal · 3 copies · chains A, B
- CA · Calcium ion · metal · chains E, B
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 | 1189 | 0.79 | 0.81 | 75 | MG, ATP |
| 2 | 454 | 0.74 | 0.84 | 40 | empty |
| 3 | 644 | 0.73 | 0.80 | 39 | empty |
| 4 | 770 | 0.73 | 0.79 | 65 | CA, MG, ATP |
| 5 | 490 | 0.72 | 0.81 | 41 | empty |
Interfaces
9 interfaces between chains.
- F–B · 1055 Ų buried · 26 hydrogen bonds · protein-nucleic
- D–A · 1026 Ų buried · 15 hydrogen bonds · protein-nucleic
- E–B · 689 Ų buried · 29 hydrogen bonds · protein-nucleic
- E–F · 666 Ų buried · 44 hydrogen bonds · nucleic-nucleic
- C–D · 597 Ų buried · 44 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 1N56 · Y-family DNA polymerase Dpo4 in complex with DNA containing abasic lesion · the same entry in another collection · chain B against B, TM-score 1.00
- Q97W02 · AlphaFold monomer V2.0 prediction for DNA polymerase IV (Q97W02) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q97W02
- Elsewhere: RCSB PDB 1N56 · PDBe 1N56 · UniProt Q97W02
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