Research workbench
Crystal Structure of Dpo4 in complex with DNA containing the major cisplatin lesion
Analyse Crystal Structure of Dpo4 in complex with DNA containing the major cisplatin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3M9M
- Type
- protein + DNA
- Length
- 368 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.9
- Source
- Sulfolobus solfataricus; SYNTHETIC CONSTRUCT
- Molecule
- DNA polymerase IV; DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*AP*AP*G)-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q97W02
- Ligands
- CTP, CPT, CA
- Pockets
- 2 · best druggability 0.80
Structure
x-ray diffraction · resolution 2.9 · 3 distinct chains · 42% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA polymerase IV (EC 2.7.7.7) | protein | 341 | 42% helix, 24% strand | Q97W02 |
| P | DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*AP*AP*G)-3') | dna | 12 | — | — |
| T | DNA (5'-D(*TP*CP*TP*GP*GP*CP*TP*TP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3') | dna | 15 | — | — |
Ligands and binding sites
- CTP · Cytidine-5'-triphosphate · ligand · chains B, T
- CPT · Cisplatin · ligand · chains T
- CA · Calcium ion · metal · 4 copies · chains B, P
- GOL · Glycerol · additive · 3 copies · chains B, T, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 951 | 0.80 | 0.82 | 73 | CTP, CA, GOL |
| 2 | 667 | 0.73 | 0.80 | 35 | empty |
Interfaces
3 interfaces between chains.
- B–T · 791 Ų buried · 14 hydrogen bonds · protein-nucleic
- P–T · 553 Ų buried · 56 hydrogen bonds · nucleic-nucleic
- B–P · 493 Ų buried · 10 hydrogen bonds · protein-nucleic
Compared structures
- 3M9M · Crystal structure of DPO4 in complex with DNA containing the major cisplatin 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 B against A, TM-score 0.97
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 3M9M · PDBe 3M9M · UniProt Q97W02
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