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DPO4 extension ternary complex with 3'-terminal primer C base opposite the 3-methylcytosine (M3C) lesion
Analyse DPO4 extension ternary complex with 3'-terminal primer C 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
- 3RBD
- Type
- protein + DNA
- Length
- 736 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*(DOC))-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q97W02
- Ligands
- DGT, CA
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 45% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA polymerase IV (EC 2.7.7.7) | protein | 341 | 45% helix, 24% strand | Q97W02 |
| D | DNA (5'-D(*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*GP*(DOC))-3') | dna | 13 | — | — |
| E | DNA (5'-D(*C*CP*TP*AP*AP*CP*(ME6) P*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*CP*C)-3') | dna | 19 | — | — |
| H | DNA (5'-D(*GP*TP*TP*GP*GP*AP*TP*GP*GP*TP*AP*GP*(DOC))-3') | dna | 11 | — | — |
| J | DNA (5'-D(*C*CP*TP*AP*AP*CP*(ME6) P*CP*TP*AP*CP*CP*AP*TP*CP*CP*AP*AP*CP*C)-3') | dna | 11 | — | — |
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
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1089 | 0.83 | 0.84 | 73 | DGT, CA |
| 2 | 1091 | 0.82 | 0.83 | 78 | DGT, CA, EPE |
| 3 | 582 | 0.73 | 0.81 | 38 | empty |
| 4 | 661 | 0.73 | 0.80 | 43 | empty |
Interfaces
7 interfaces between chains.
- A–E · 1115 Ų buried · 22 hydrogen bonds · protein-nucleic
- B–J · 769 Ų buried · 21 hydrogen bonds · protein-nucleic
- A–D · 664 Ų buried · 18 hydrogen bonds · protein-nucleic
- B–H · 612 Ų buried · 16 hydrogen bonds · protein-nucleic
- D–E · 574 Ų buried · 49 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 3RBD · Dpo4 extension ternary complex with 3'-terminal primer C base opposite the… · the same entry in another collection · chain E against E, 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 3RBD · PDBe 3RBD · UniProt Q97W02
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