MolNFT v1 · #34356 · protein + DNA
Crystal structure of uracil-DNA glycosylase in complex with AP:G containing DNA
2DDG · 5'-D(*AP*TP*GP*TP*TP*GP*CP*(D1P)P*TP*TP*AP*GP*TP*CP*C)-3': “Crystal structure of uracil-DNA glycosylase in complex with AP:G containing DNA”. X-ray diffraction, 3 ligands (ORP, SF4, 2HP), 1 pocket (best druggability 0.78). MolNFT v1…
- PDB
- 2DDG
- Type
- protein + DNA
- Length
- 247 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*AP*TP*GP*TP*TP*GP*CP*(D1P)P*TP*TP*AP*GP*TP*CP*C)-3'…
- EC
- 3.2.2.-
- Ligands
- ORP, SF4, 2HP
- Pockets
- 1 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | 5'-D(*AP*TP*GP*TP*TP*GP*CP*(D1P)P*TP*TP*AP*GP*TP*CP*C)-3' | dna | 14 | — | — |
| D | 5'-D(*GP*GP*AP*CP*TP*AP*AP*GP*GP*CP*AP*AP*CP*A)-3' | dna | 14 | — | — |
| A | Uracil-DNA glycosylase (EC 3.2.2.-) | protein | 219 | 38% helix, 13% strand | — |
Ligands and binding sites
- ORP · 2-deoxy-5-phosphono-ribose · ligand · chains C, A
- SF4 · Iron/sulfur cluster · ligand · chains A
- 2HP · Dihydrogenphosphate ion · ion · 2 copies · chains D, A
- EOH · Ethanol · additive · 4 copies · chains A, C
- ACT · Acetate ion · additive · 2 copies · chains C, D, A
- GOL · Glycerol · additive · chains A
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 | 989 | 0.78 | 0.80 | 93 | ORP, ACT, 2HP, EOH |
Interfaces
3 interfaces between chains.
- C–D · 614 Ų buried · 49 hydrogen bonds · nucleic-nucleic
- C–A · 577 Ų buried · 11 hydrogen bonds · protein-nucleic
- D–A · 538 Ų buried · 11 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2DDG · Crystal structure of uracil-DNA glycosylase in complex with AP:G containing DNA · the same entry in another collection · chain C against C, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 2DDG · PDBe 2DDG
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