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Crystal structure of APOBEC3G Catalytic domain complex with ssDNA containing 2'-deoxy Zebularine.

Analyse Crystal structure of APOBEC3G Catalytic domain complex with ssDNA containing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7UXD
Type: protein + DNA
Length: 199 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.5
Source: Homo sapiens; synthetic construct
Molecule: DNA dC->dU-editing enzyme APOBEC-3G; DNA (5'-D(*AP*AP*TP*CP*CP*(DDN)P*AP*AP*A)-3')
EC: 3.5.4.38
UniProt: Q9HC16
Ligands: ZN

Structure

x-ray diffraction · resolution 1.5 · 2 distinct chains · 38% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	DNA dC->dU-editing enzyme APOBEC-3G (EC 3.5.4.38)	protein	190	38% helix, 27% strand	Q9HC16
B	DNA (5'-D(APAPTPCPCP(DDN)PAPAP*A)-3')	dna	9	—	—

Ligands and binding sites

ZN · Zinc ion · metal · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Interfaces

1 interface between chains.

A–B · 799 Å² buried · 25 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 1 modified (nucleotide modification).

Compared structures

Q9HC16 · AlphaFold monomer V2.0 prediction for DNA dc->du-editing enzyme apobec-3G (Q9HC16) · a predicted model of the same protein · chain A against A, TM-score 0.97

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q9HC16
Elsewhere: RCSB PDB 7UXD · PDBe 7UXD · UniProt Q9HC16

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