MolNFT v1 · #142914 · protein + DNA
Complex form of uracil DNA glycosylase X and uracil-DNA.
6AJO · Uracil DNA glycosylase superfamily protein: “Complex form of uracil DNA glycosylase X and uracil-DNA.”. X-ray diffraction, 4 ligands (ORP, SF4, URA), 2 pockets (best druggability 0.52). MolNFT v1 #142914 on GenesisL1: 3D structure…
- PDB
- 6AJO
- Type
- protein + DNA
- Length
- 204 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uracil DNA glycosylase superfamily protein; DNA (5'-D(P*(ORP)P*TP*T)-3')
- UniProt
- A0QP43
- Ligands
- ORP, SF4, URA, PO4
- Pockets
- 2 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uracil DNA glycosylase superfamily protein | protein | 202 | 45% helix, 13% strand | A0QP43 |
| F | DNA (5'-D(P*(ORP)P*TP*T)-3') | dna | 2 | — | — |
Ligands and binding sites
- ORP · 2-deoxy-5-phosphono-ribose · ligand · chains A, F
- SF4 · Iron/sulfur cluster · ligand · chains A
- URA · Uracil · ligand · chains A
- PO4 · Phosphate ion · ion · chains A, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 127 | 0.52 | 0.81 | 22 | ORP, URA |
| 2 | 57 | 0.35 | 0.78 | 19 | PO4 |
Interfaces
1 interface between chains.
- A–F · 350 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6AJO · Complex form of Uracil DNA glycosylase X and uracil-DNA. · the same entry in another collection · chain A against A, 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
- Every structure of UniProt A0QP43
- Elsewhere: RCSB PDB 6AJO · PDBe 6AJO · UniProt A0QP43
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