Research workbench
Y-family DNA polymerase chimera dbh-DPO4-DPO4 #1
Analyse Y-family DNA polymerase chimera dbh-DPO4-DPO4 #1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4F4W
- Type
- protein + DNA
- Length
- 740 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*C)-3'); DNA (5'…
- EC
- 2.7.7.7
- UniProt
- Q4JB80, Q97W02
- Ligands
- DCP, CA
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 3 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 | 342 | 45% helix, 25% strand | Q4JB80, Q97W02 |
| P, E | DNA (5'-D(*GP*GP*CP*AP*CP*TP*GP*AP*TP*CP*GP*GP*C)-3') | dna | 13 | — | — |
| T, F | DNA (5'- D(*TP*TP*AP*CP*GP*GP*CP*CP*GP*AP*TP*CP*AP*GP*TP*GP*CP*C)-3') | dna | 15 | — | — |
Ligands and binding sites
- DCP · 2'-deoxycytidine-5'-triphosphate · ligand · 2 copies · chains A, P, T, B, E, F
- CA · Calcium ion · metal · 4 copies · chains A, P, B, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1112 | 0.78 | 0.80 | 74 | DCP, CA |
| 2 | 1134 | 0.77 | 0.80 | 78 | DCP, CA |
| 3 | 341 | 0.70 | 0.83 | 40 | empty |
| 4 | 202 | 0.61 | 0.83 | 20 | empty |
| 5 | 197 | 0.61 | 0.82 | 27 | empty |
Interfaces
9 interfaces between chains.
- A–T · 1000 Ų buried · 21 hydrogen bonds · protein-nucleic
- B–F · 974 Ų buried · 25 hydrogen bonds · protein-nucleic
- P–T · 596 Ų buried · 48 hydrogen bonds · nucleic-nucleic
- E–F · 591 Ų buried · 46 hydrogen bonds · nucleic-nucleic
- B–E · 479 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 4F4W · Y-family DNA polymerase chimera Dbh-Dpo4-Dpo4 #1 · the same entry in another collection · chain F against F, 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 4F4W · PDBe 4F4W · UniProt Q4JB80 · UniProt Q97W02
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