Research workbench
Y-family DNA polymerase chimera DPO4-DPO4-dbh
Analyse Y-family DNA polymerase chimera DPO4-DPO4-dbh in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4F4Z
- Type
- protein + DNA
- Length
- 732 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase IV; DNA (5'-D(*AP*GP*GP*GP*GP*GP*AP*AP*GP*CP*CP*G)-3'); DNA (5'…
- EC
- 2.7.7.7
- UniProt
- Q97W02, Q4JB80
- Ligands
- CA
- Pockets
- 8 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 45% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA polymerase IV (EC 2.7.7.7) | protein | 341 | 45% helix, 23% strand | Q97W02, Q4JB80 |
| A | DNA polymerase IV (EC 2.7.7.7) | protein | 342 | 45% helix, 25% strand | Q97W02, Q4JB80 |
| P, C | DNA (5'-D(*AP*GP*GP*GP*GP*GP*AP*AP*GP*CP*CP*G)-3') | dna | 12 | — | — |
| T | DNA (5'- D(*TP*TP*CP*CP*GP*CP*CP*CP*GP*GP*CP*TP*TP*CP*CP*CP*CP*CP*T)-3') | dna | 13 | — | — |
| D | DNA (5'- D(*TP*TP*CP*CP*GP*CP*CP*CP*GP*GP*CP*TP*TP*CP*CP*CP*CP*CP*T)-3') | dna | 12 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains B, C, A, P
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1079 | 0.83 | 0.85 | 96 | empty |
| 2 | 1165 | 0.78 | 0.80 | 75 | empty |
| 3 | 224 | 0.64 | 0.83 | 34 | empty |
| 4 | 212 | 0.56 | 0.79 | 30 | empty |
| 5 | 219 | 0.49 | 0.75 | 31 | CA |
Interfaces
7 interfaces between chains.
- A–T · 849 Ų buried · 17 hydrogen bonds · protein-nucleic
- B–C · 715 Ų buried · 12 hydrogen bonds · protein-nucleic
- B–D · 686 Ų buried · 4 hydrogen bonds · protein-nucleic
- A–P · 686 Ų buried · 8 hydrogen bonds · protein-nucleic
- P–T · 546 Ų buried · 55 hydrogen bonds · nucleic-nucleic
Compared structures
- 4F4Z · Y-family DNA polymerase chimera Dpo4-Dpo4-Dbh · the same entry in another collection · chain D against D, TM-score 1.00
- Q4JB80 · AlphaFold monomer V2.0 prediction for DNA polymerase IV (Q4JB80) · a predicted model of the same protein · chain A against A, TM-score 0.96
- Q97W02 · AlphaFold monomer V2.0 prediction for DNA polymerase IV (Q97W02) · a predicted model of the same protein · chain A against A, TM-score 0.96
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
- Every structure of UniProt Q4JB80
- Elsewhere: RCSB PDB 4F4Z · PDBe 4F4Z · UniProt Q97W02 · UniProt Q4JB80
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