MolNFT v1 · #117628 · protein + DNA
Ternary structure of DPO4 bound to G in the template base paired with incoming dttp
5EDW · DNA polymerase IV: “Ternary structure of DPO4 bound to G in the template base paired with incoming dttp”. X-ray diffraction, 2 ligands (TTP, CA), 2 pockets (best druggability 0.83). MolNFT v1 #117628 on GenesisL1: 3D structure…
- PDB
- 5EDW
- Type
- protein + DNA
- Length
- 373 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase IV; DNA (5'- D(*CP*TP*AP*AP*CP*GP*GP*GP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3'…
- EC
- 2.7.7.7
- UniProt
- Q97W02
- Ligands
- TTP, CA
- Pockets
- 2 · best druggability 0.83
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 |
| T | DNA (5'- D(*CP*TP*AP*AP*CP*GP*GP*GP*AP*TP*CP*CP*TP*TP*CP*CP*CP*CP*C)-3') | dna | 19 | — | — |
| P | DNA (5'-D(*GP*GP*GP*GP*GP*AP*AP*GP*GP*AP*TP*TP*C)-3') | dna | 13 | — | — |
Ligands and binding sites
- TTP · Thymidine-5'-triphosphate · ligand · chains A, T, P
- CA · Calcium ion · metal · 3 copies · chains A, P
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 | 986 | 0.83 | 0.84 | 65 | CA, TTP |
| 2 | 657 | 0.74 | 0.80 | 41 | empty |
Interfaces
3 interfaces between chains.
- A–T · 1198 Ų buried · 22 hydrogen bonds · protein-nucleic
- T–P · 578 Ų buried · 63 hydrogen bonds · nucleic-nucleic
- A–P · 568 Ų buried · 20 hydrogen bonds · protein-nucleic
Compared structures
- 5EDW · Ternary structure of Dpo4 bound to G in the template base paired with incoming dTTP · 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 5EDW · PDBe 5EDW · UniProt Q97W02
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