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
- 2RDI
- Type
- protein
- Length
- 336 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase IV
- EC
- 2.7.7.7
- UniProt
- Q97W02
- Pockets
- 1 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 46% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase IV (EC 2.7.7.7) | protein | 336 | 46% helix, 25% strand | Q97W02 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 798 | 0.71 | 0.76 | 77 | empty |
Compared structures
- 2RDI · Snapshots of a Y-family DNA polymerase in replication: Dpo4 in apo and binary/ternary… · the same entry in another collection · chain A against A, 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 0.73
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 2RDI · PDBe 2RDI · UniProt Q97W02
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