Research workbench
Crystal structure of se-met DPB4-DPB3
Analyse Crystal structure of se-met DPB4-DPB3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Y27
- Type
- protein
- Length
- 190 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA polymerase epsilon subunit D; Putative transcription factor C16C4.22
- EC
- 2.7.7.7
- UniProt
- P87174, C6Y4D0
Structure
x-ray diffraction · 2 distinct chains · 66% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA polymerase epsilon subunit D (EC 2.7.7.7) | protein | 98 | 76% helix, 3% strand | P87174 |
| B | Putative transcription factor C16C4.22 | protein | 92 | 57% helix, 3% strand | C6Y4D0 |
Ligands and binding sites
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Interfaces
1 interface between chains.
- A–B · 2497 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (engineered).
Compared structures
- 5Y27 · Crystal structure of Se-Met Dpb4-Dpb3 · the same entry in another collection · chain A against A, TM-score 1.00
- P87174 · AlphaFold monomer V2.0 prediction for DNA polymerase epsilon subunit D (P87174) · a predicted model of the same protein · chain A against A, TM-score 0.97
- C6Y4D0 · AlphaFold monomer V2.0 prediction for DNA polymerase epsilon subunit C (C6Y4D0) · a predicted model of the same protein · chain B against A, TM-score 0.91
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 P87174
- Every structure of UniProt C6Y4D0
- Elsewhere: RCSB PDB 5Y27 · PDBe 5Y27 · UniProt P87174 · UniProt C6Y4D0
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