Research workbench
Y-family DNA polymerase chimera dbh-DPO4-dbh
Analyse Y-family DNA polymerase chimera dbh-DPO4-dbh in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4F4Y
- Type
- protein + DNA
- Length
- 754 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase IV; DNA (5'-D(*GP*GP*CP*AP*CP*TP*GP*AP*TP*CP*GP*GP*GP*CP*CP*C)- 3'); DNA…
- EC
- 2.7.7.7
- UniProt
- Q4JB80, Q97W02
- Ligands
- DCP, CA
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA polymerase IV (EC 2.7.7.7) | protein | 343 | 40% helix, 25% strand | Q4JB80, Q97W02 |
| C, P | DNA (5'-D(*GP*GP*CP*AP*CP*TP*GP*AP*TP*CP*GP*GP*GP*CP*CP*C)- 3') | dna | 16 | — | — |
| D, T | DNA (5'- D(*TP*TP*AP*CP*GP*CP*CP*CP*TP*GP*AP*TP*CP*AP*GP*TP*GP*CP*C)-3') | dna | 18 | — | — |
Ligands and binding sites
- DCP · 2'-deoxycytidine-5'-triphosphate · ligand · 2 copies · chains A, P, T, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, P, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 943 | 0.78 | 0.81 | 77 | CA, DCP |
| 2 | 1063 | 0.76 | 0.79 | 85 | DCP, CA |
| 3 | 407 | 0.68 | 0.80 | 45 | empty |
| 4 | 206 | 0.58 | 0.80 | 26 | empty |
| 5 | 189 | 0.53 | 0.78 | 24 | empty |
Interfaces
7 interfaces between chains.
- A–T · 1083 Ų buried · 20 hydrogen bonds · protein-nucleic
- B–D · 1047 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–P · 826 Ų buried · 18 hydrogen bonds · protein-nucleic
- B–C · 808 Ų buried · 11 hydrogen bonds · protein-nucleic
- C–D · 760 Ų buried · 71 hydrogen bonds · nucleic-nucleic
Compared structures
- 4F4Y · Y-family DNA polymerase chimera Dbh-Dpo4-Dbh · the same entry in another collection · chain T against T, 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 0.98
- 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 Q4JB80
- Every structure of UniProt Q97W02
- Elsewhere: RCSB PDB 4F4Y · PDBe 4F4Y · UniProt Q4JB80 · UniProt Q97W02
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