Research workbench
DPO4 post-insertion complex with the N-(deoxyguanosin-8-yl)-1- aminopyrene lesion
Analyse DPO4 post-insertion complex with the N-(deoxyguanosin-8-yl)-1- aminopyrene… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FBT
- 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 primer; DNA template
- EC
- 2.7.7.7
- UniProt
- Q97W02
- Ligands
- DGT, GTP, CA
- Pockets
- 3 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase IV (EC 2.7.7.7) | protein | 341 | 45% helix, 25% strand | Q97W02 |
| P | DNA primer | dna | 13 | — | — |
| T | DNA template | dna | 16 | — | — |
Ligands and binding sites
- DGT · 2'-deoxyguanosine-5'-triphosphate · ligand · chains A, T
- GTP · Guanosine-5'-triphosphate · ligand · chains P, T
- CA · Calcium ion · metal · 3 copies · chains A
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 | 1199 | 0.74 | 0.77 | 71 | DGT, CA, GTP |
| 2 | 330 | 0.70 | 0.83 | 30 | empty |
| 3 | 95 | 0.36 | 0.76 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–T · 817 Ų buried · 22 hydrogen bonds · protein-nucleic
- P–T · 612 Ų buried · 54 hydrogen bonds · nucleic-nucleic
- A–P · 527 Ų buried · 14 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 4FBT · Dpo4 post-insertion complex with the N-(deoxyguanosin-8-yl)-1-aminopyrene lesion · 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 0.95
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 4FBT · PDBe 4FBT · UniProt Q97W02
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