Research workbench
Ternary complex of hne adduct modified DNA (5'-txg-3' vs 14-mer) with DPO4 and incoming ddtp
Analyse Ternary complex of hne adduct modified DNA (5'-txg-3' vs 14-mer) with DPO4 and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3T5K
- Type
- protein + DNA
- Length
- 372 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase IV; DNA (5'-D(*CP*AP*TP*(HN0) P*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3')…
- EC
- 2.7.7.7
- UniProt
- Q97W02
- Ligands
- DTP, CA
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase IV (EC 2.7.7.7) | protein | 341 | 43% helix, 25% strand | Q97W02 |
| B | DNA (5'-D(*CP*AP*TP*(HN0) P*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3') | dna | 17 | — | — |
| C | DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*CP*C)-3') | dna | 14 | — | — |
Ligands and binding sites
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · chains A, B, C
- CA · Calcium ion · metal · 3 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 617 | 0.77 | 0.83 | 43 | empty |
| 2 | 609 | 0.74 | 0.81 | 40 | empty |
| 3 | 348 | 0.63 | 0.79 | 36 | DTP, CA |
| 4 | 330 | 0.58 | 0.76 | 29 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1080 Ų buried · 29 hydrogen bonds · protein-nucleic
- B–C · 633 Ų buried · 57 hydrogen bonds · nucleic-nucleic
- A–C · 624 Ų buried · 17 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 3T5K · Ternary complex of HNE Adduct modified DNA (5'-TXG-3' vs 14-mer) with Dpo4 and incoming… · the same entry in another collection · chain A against A, 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 0.98
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 Q97W02
- Elsewhere: RCSB PDB 3T5K · PDBe 3T5K · UniProt Q97W02
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