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Ternary crystal structures of a Y-family DNA polymerase DPO4 from sulfolobus solfataricus in complex with DNA and (-)3TC-ppnp
Analyse Ternary crystal structures of a Y-family DNA polymerase DPO4 from sulfolobus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QWD
- Type
- protein + DNA
- Length
- 370 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase IV; DNA (5'-D(P*GP*GP*CP*TP*AP*CP*AP*GP*GP*AP*CP*TP*C)-3'); DNA (5'…
- EC
- 2.7.7.7
- UniProt
- Q97W02
- Ligands
- 3TT, CA
- Pockets
- 3 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase IV (EC 2.7.7.7) | protein | 341 | 44% helix, 25% strand | Q97W02 |
| C | DNA (5'-D(P*GP*GP*CP*TP*AP*CP*AP*GP*GP*AP*CP*TP*C)-3') | dna | 13 | — | — |
| D | DNA (5'- D(P*CP*AP*GP*GP*AP*GP*TP*CP*CP*TP*GP*TP*AP*GP*CP*C)-3') | dna | 16 | — | — |
Ligands and binding sites
- 3TT · [[[[(2R,5S)-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-1,3-oxathiolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]amino]phosphonic acid · ligand · chains A, C, D
- CA · Calcium ion · metal · 4 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1017 | 0.82 | 0.83 | 64 | 3TT, CA |
| 2 | 696 | 0.73 | 0.80 | 40 | empty |
| 3 | 65 | 0.33 | 0.75 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–D · 1006 Ų buried · 20 hydrogen bonds · protein-nucleic
- C–D · 575 Ų buried · 49 hydrogen bonds · nucleic-nucleic
- A–C · 565 Ų buried · 15 hydrogen bonds · protein-nucleic
Compared structures
- 4QWD · TERNARY CRYSTAL STRUCTURES of A Y-FAMILY DNA POLYMERASE DPO4 FROM SULFOLOBUS SOLFATARICUS… · 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 4QWD · PDBe 4QWD · UniProt Q97W02
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