Research workbench
Ternary complex of Y-family DNA polymerase DPO4 with (5'S)-8,5'-cyclo- 2'-deoxyguanosine and dttp
Analyse Ternary complex of Y-family DNA polymerase DPO4 with (5'S)-8,5'-cyclo… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4TQR
- 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(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*T)-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q97W02
- Ligands
- DOC, TTP, MG, CA
- Pockets
- 2 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase IV (EC 2.7.7.7) | protein | 342 | 41% helix, 24% strand | Q97W02 |
| P | DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*T)-3') | dna | 12 | — | — |
| T | DNA (5'-D(*TP*CP*AP*CP*(2LF) P*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3') | dna | 18 | — | — |
Ligands and binding sites
- DOC · 2',3'-dideoxycytidine-5'-monophosphate · ligand · chains A, P, T
- TTP · Thymidine-5'-triphosphate · ligand · chains A, T
- MG · Magnesium ion · metal · 3 copies · chains A, T
- CA · Calcium ion · metal · 2 copies · chains T
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 | 477 | 0.70 | 0.81 | 35 | empty |
| 2 | 1106 | 0.69 | 0.74 | 82 | MG, DOC, CA, TTP |
Interfaces
3 interfaces between chains.
- A–T · 927 Ų buried · 30 hydrogen bonds · protein-nucleic
- P–T · 525 Ų buried · 43 hydrogen bonds · nucleic-nucleic
- A–P · 423 Ų buried · 9 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 covalent, 1 modified (covalent ligand, nucleotide modification).
Compared structures
- 4TQR · Ternary complex of Y-family DNA polymerase Dpo4 with (5'S)-8,5'-Cyclo-2'-deoxyguanosine… · 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 0.88
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 4TQR · PDBe 4TQR · UniProt Q97W02
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.