Research workbench
DPO4 extension ternary complex with 3'-terminal primer T base opposite the 1-methylguanine (M1G) lesion
Analyse DPO4 extension ternary complex with 3'-terminal primer T base opposite the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3RAX
- Type
- protein + DNA
- Length
- 743 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase IV; DNA (5'-D(*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*GP*(2DT))-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q97W02
- Ligands
- DGT, CA
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA polymerase IV (EC 2.7.7.7) | protein | 341 | 45% helix, 25% strand | Q97W02 |
| D, H | DNA (5'-D(*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*GP*(2DT))-3') | dna | 13 | — | — |
| E | DNA (5'-D(*CP*CP*TP*AP*AP*CP*(MG1) P*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*CP*C)-3') | dna | 18 | — | — |
| J | DNA (5'-D(*CP*CP*TP*AP*AP*CP*(MG1) P*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*CP*C)-3') | dna | 17 | — | — |
Ligands and binding sites
- DGT · 2'-deoxyguanosine-5'-triphosphate · ligand · 2 copies · chains A, D, E, B, H, J
- CA · Calcium ion · metal · 6 copies · chains A, D, B, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1124 | 0.81 | 0.83 | 72 | DGT, CA |
| 2 | 1169 | 0.81 | 0.82 | 79 | DGT, CA |
| 3 | 557 | 0.71 | 0.80 | 45 | empty |
| 4 | 446 | 0.71 | 0.82 | 44 | empty |
| 5 | 285 | 0.57 | 0.77 | 40 | empty |
Interfaces
7 interfaces between chains.
- A–E · 1016 Ų buried · 23 hydrogen bonds · protein-nucleic
- B–J · 977 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–B · 627 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 608 Ų buried · 49 hydrogen bonds · nucleic-nucleic
- H–J · 605 Ų buried · 53 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 3RAX · Dpo4 extension ternary complex with 3'-terminal primer T base opposite the… · the same entry in another collection · chain J against J, TM-score 1.00
- Q97W02 · AlphaFold monomer V2.0 prediction for DNA polymerase IV (Q97W02) · a predicted model of the same protein · chain B 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 3RAX · PDBe 3RAX · UniProt Q97W02
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