Research workbench
Y-family DNA polymerase chimera dbh-dbh-DPO4
Analyse Y-family DNA polymerase chimera dbh-dbh-DPO4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4F50
- Type
- protein + DNA
- Length
- 360 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase IV; DNA (5'-D(*GP*GP*GP*AP*AP*GP*CP*CP*GP*GP*C)-3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q4JB80, Q97W02
- Ligands
- CA
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase IV (EC 2.7.7.7) | protein | 337 | 42% helix, 23% strand | Q4JB80, Q97W02 |
| P | DNA (5'-D(*GP*GP*GP*AP*AP*GP*CP*CP*GP*GP*C)-3') | dna | 11 | — | — |
| T | DNA (5'-D(*CP*CP*GP*CP*CP*T*GP*GP*CP*TP*TP*CP*CP*C)-3') | dna | 12 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 835 | 0.75 | 0.80 | 67 | CA |
| 2 | 367 | 0.56 | 0.75 | 22 | empty |
| 3 | 90 | 0.37 | 0.76 | 17 | empty |
| 4 | 92 | 0.37 | 0.76 | 20 | empty |
Interfaces
3 interfaces between chains.
- P–T · 494 Ų buried · 44 hydrogen bonds · nucleic-nucleic
- A–P · 450 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–T · 355 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 4F50 · Y-family DNA polymerase chimera Dbh-Dbh-Dpo4 · the same entry in another collection · chain A against A, 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 0.79
- Q97W02 · AlphaFold monomer V2.0 prediction for DNA polymerase IV (Q97W02) · a predicted model of the same protein · chain A against A, TM-score 0.77
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 Q4JB80
- Every structure of UniProt Q97W02
- Elsewhere: RCSB PDB 4F50 · PDBe 4F50 · UniProt Q4JB80 · UniProt Q97W02
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