MolNFT v1 · #105160 · protein + DNA
Ternary crystal structures of a Y-family DNA polymerase DPO4 from sulfobus solfataricus in comples with DNA and L-dcdp
4QWC · DNA polymerase IV: “Ternary crystal structures of a Y-family DNA polymerase DPO4 from sulfobus solfataricus in comples with DNA…”. X-ray diffraction, 2 ligands (LTP, CA), 6 pockets (best druggability 0.79). MolNFT v1 #105160 on…
- PDB
- 4QWC
- Type
- protein + DNA
- Length
- 740 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase IV; DNA (5'-D(*GP*GP*CP*TP*AP*CP*AP*GP*GP*AP*CP*TP*C)-3'); DNA (5'…
- EC
- 2.7.7.7
- UniProt
- Q97W02
- Ligands
- LTP, CA
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | DNA polymerase IV (EC 2.7.7.7) | protein | 342 | 44% helix, 25% strand | Q97W02 |
| B, E | DNA (5'-D(*GP*GP*CP*TP*AP*CP*AP*GP*GP*AP*CP*TP*C)-3') | dna | 13 | — | — |
| C, F | DNA (5'- D(*TP*TP*CP*AP*GP*GP*AP*GP*TP*CP*CP*TP*GP*TP*AP*GP*CP*C)-3') | dna | 15 | — | — |
Ligands and binding sites
- LTP · 4-amino-1-{2-deoxy-5-O-[(R)-hydroxy(phosphonooxy)phosphoryl]-beta-L-erythro-pentofuranosyl}pyrimidin-2(1H)-one · ligand · 2 copies · chains A, B, C, D, E, F
- CA · Calcium ion · metal · 5 copies · chains A, D, E
- ACT · Acetate ion · additive · 3 copies · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1147 | 0.79 | 0.81 | 79 | CA, LTP |
| 2 | 943 | 0.79 | 0.81 | 65 | CA, LTP |
| 3 | 716 | 0.74 | 0.80 | 43 | empty |
| 4 | 494 | 0.70 | 0.80 | 41 | empty |
| 5 | 87 | 0.35 | 0.75 | 19 | empty |
Interfaces
8 interfaces between chains.
- A–C · 922 Ų buried · 20 hydrogen bonds · protein-nucleic
- D–F · 886 Ų buried · 17 hydrogen bonds · protein-nucleic
- B–C · 582 Ų buried · 51 hydrogen bonds · nucleic-nucleic
- E–F · 573 Ų buried · 36 hydrogen bonds · nucleic-nucleic
- D–E · 552 Ų buried · 17 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 4QWC · Ternary Crystal Structures of a Y-family DNA polymerase DPO4 from Sulfobus Solfataricus… · the same entry in another collection · chain F against F, TM-score 1.00
- Q97W02 · AlphaFold monomer V2.0 prediction for DNA polymerase IV (Q97W02) · a predicted model of the same protein · chain D 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 4QWC · PDBe 4QWC · UniProt Q97W02
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