MolNFT v1 · #5588 · protein + DNA
Uracil-DNA glycosylase bound to DNA containing a 4'-thio- 2'DEOXYURIDINE analog product
1EMJ · DNA (5'-D(*TP*GP*TP*(ASU)P*AP*TP*CP*TP*T)-3'): “Uracil-DNA glycosylase bound to DNA containing a 4'-thio- 2'DEOXYURIDINE analog product”. X-ray diffraction, 1 ligand (URA), 2 pockets (best druggability 0.47). MolNFT v1 #5588 on…
- PDB
- 1EMJ
- Type
- protein + DNA
- Length
- 242 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*TP*GP*TP*(ASU)P*AP*TP*CP*TP*T)-3'); DNA…
- EC
- 3.2.2.3
- UniProt
- P13051
- Ligands
- URA
- Pockets
- 2 · best druggability 0.47
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | DNA (5'-D(*TP*GP*TP*(ASU)P*AP*TP*CP*TP*T)-3') | dna | 9 | — | — |
| C | DNA (5'-D(*AP*AP*AP*GP*AP*TP*AP*AP*CP*A)-3') | dna | 10 | — | — |
| A | Uracil-DNA glycosylase (EC 3.2.2.3) | protein | 223 | 40% helix, 11% strand | P13051 |
Ligands and binding sites
- URA · Uracil · ligand · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 247 | 0.47 | 0.74 | 27 | empty |
| 2 | 96 | 0.34 | 0.74 | 13 | empty |
Interfaces
3 interfaces between chains.
- B–A · 621 Ų buried · 14 hydrogen bonds · protein-nucleic
- B–C · 358 Ų buried · 21 hydrogen bonds · nucleic-nucleic
- C–A · 189 Ų buried · 1 hydrogen bond · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 1EMJ · Uracil-DNA glycosylase bound to DNA containing a 4'-thio-2'DEOXYURIDINE analog product · the same entry in another collection · chain B against B, TM-score 1.00
- P13051 · AlphaFold monomer V2.0 prediction for uracil-DNA glycosylase (P13051) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P13051
- Elsewhere: RCSB PDB 1EMJ · PDBe 1EMJ · UniProt P13051
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