Research workbench
Snapshots of a Y-family DNA polymerase in replication: DPO4 in apo and BINARY/TERNARY complex forms
Analyse Snapshots of a Y-family DNA polymerase in replication: DPO4 in apo and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2RDJ
- Type
- protein + DNA
- Length
- 741 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*DGP*DGP*DGP*DAP*DCP*DCP*DCP*DTP*DTP*DCP*DGP*DAP*DAP*DT)-3'); DNA (5'…
- EC
- 2.7.7.7
- UniProt
- Q97W02
- Ligands
- TMP, CA
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 45% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, E | DNA (5'- D(*DGP*DGP*DGP*DAP*DCP*DCP*DCP*DTP*DTP*DCP*DGP*DAP*DAP*DT)-3') | dna | 14 | — | — |
| D | DNA (5'- D(P*DTP*DTP*DAP*DTP*DTP*DCP*DGP*DAP*DAP*DGP*DGP*DGP*DTP*DCP*DCP*DC)- 3') | dna | 16 | — | — |
| F | DNA (5'- D(P*DTP*DAP*DTP*DTP*DCP*DGP*DAP*DAP*DGP*DGP*DGP*DTP*DCP*DCP*DC)-3') | dna | 15 | — | — |
| A, B | DNA polymerase IV (EC 2.7.7.7) | protein | 341 | 45% helix, 25% strand | Q97W02 |
Ligands and binding sites
- TMP · Thymidine-5'-phosphate · ligand · chains C, D, A
- CA · Calcium ion · metal · 4 copies · chains C, A, E, B
- GOL · Glycerol · additive · chains C, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1083 | 0.81 | 0.82 | 79 | CA, TMP |
| 2 | 1072 | 0.78 | 0.80 | 68 | empty |
| 3 | 656 | 0.73 | 0.80 | 47 | empty |
| 4 | 607 | 0.72 | 0.80 | 42 | empty |
| 5 | 229 | 0.48 | 0.75 | 31 | CA |
Interfaces
8 interfaces between chains.
- D–A · 984 Ų buried · 21 hydrogen bonds · protein-nucleic
- F–B · 937 Ų buried · 24 hydrogen bonds · protein-nucleic
- E–B · 752 Ų buried · 19 hydrogen bonds · protein-nucleic
- C–A · 680 Ų buried · 17 hydrogen bonds · protein-nucleic
- E–F · 624 Ų buried · 63 hydrogen bonds · nucleic-nucleic
Compared structures
- 2RDJ · Snapshots of a Y-family DNA polymerase in replication: Dpo4 in apo and binary/ternary… · the same entry in another collection · chain B against B, 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 2RDJ · PDBe 2RDJ · UniProt Q97W02
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