MolNFT v1 · #106811 · protein + DNA
Ternary complex of Y-family DNA polymerase DPO4 with (5'S)-8,5'-cyclo- 2'-deoxyguanosine and dctp
4TQS · DNA polymerase IV: “Ternary complex of Y-family DNA polymerase DPO4 with (5'S)-8,5'-cyclo- 2'-deoxyguanosine and dctp”. X-ray diffraction, 3 ligands (DCP, DOC, MG), 7 pockets (best druggability 0.81). MolNFT v1 #106811 on GenesisL1…
- PDB
- 4TQS
- Type
- protein + DNA
- Length
- 736 residues
- Chains
- 6
- 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
- DCP, DOC, MG
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 5 distinct chains · 44% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase IV (EC 2.7.7.7) | protein | 342 | 43% helix, 22% strand | Q97W02 |
| B | DNA polymerase IV (EC 2.7.7.7) | protein | 343 | 44% helix, 24% strand | Q97W02 |
| C, P | DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*T)-3') | dna | 12 | — | — |
| D | DNA (5'-D(P*TP*CP*AP*CP*(2LF) P*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3') | dna | 13 | — | — |
| T | DNA (5'-D(P*TP*CP*AP*CP*(2LF) P*GP*AP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3') | dna | 14 | — | — |
Ligands and binding sites
- DCP · 2'-deoxycytidine-5'-triphosphate · ligand · 2 copies · chains A, P, T, B, C, D
- DOC · 2',3'-dideoxycytidine-5'-monophosphate · ligand · 2 copies · chains B, C, D, A, P, T
- MG · Magnesium ion · metal · 4 copies · chains A, 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 859 | 0.81 | 0.83 | 87 | DCP, MG, DOC |
| 2 | 857 | 0.77 | 0.81 | 68 | DCP, MG, DOC |
| 3 | 540 | 0.73 | 0.82 | 50 | empty |
| 4 | 475 | 0.70 | 0.81 | 40 | empty |
| 5 | 78 | 0.37 | 0.77 | 15 | empty |
Interfaces
7 interfaces between chains.
- B–D · 662 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–T · 652 Ų buried · 13 hydrogen bonds · protein-nucleic
- B–C · 568 Ų buried · 12 hydrogen bonds · protein-nucleic
- P–T · 545 Ų buried · 50 hydrogen bonds · nucleic-nucleic
- C–D · 545 Ų buried · 55 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 covalent, 1 modified (covalent ligand, nucleotide modification).
Compared structures
- 4TQS · Ternary complex of Y-family DNA polymerase Dpo4 with (5'S)-8,5'-Cyclo-2'-deoxyguanosine… · the same entry in another collection · chain T against T, 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 0.95
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 4TQS · PDBe 4TQS · UniProt Q97W02
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