2KQD: First PBZ domain of human APLF protein

First PBZ domain of human APLF protein in complex with ribofuranosyladenosine. Determined by solution NMR. Released 19 Jan 2010.

Method: Solution NMR
Organism: Homo sapiens
Chains: 1
Atoms: 445
Mol. weight: 10.54 kDa
Ligands: ZN, ADN, RIB
Released: 19 Jan 2010

Explore 2KQD in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2KQD contains 4 α-helices and 2 β-strands across 1 chain. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	376	1
β-strand	377-378	2	1
α-helix	379	1
α-helix	382-384	3
α-helix	392-395	4
β-strand	396-397	2	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Aprataxin and PNK-like factor	A	protein	89	Homo sapiens	Q8IW19 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>2KQD_1 Aprataxin and PNK-like factor (chains A)
GPLGSGSEGNKVKRTSCMYGANCYRKNPVHFQHFSHPGDSDYGGVQIVGQDETDDRPECP
YGPSCYRKNPQHKIEYRHNTLPVRNVLDE

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
ADN	Adenosine	C10 H13 N5 O4	1
RIB	alpha-D-ribofuranose	C5 H10 O5	1

Primary citation

Solution structures of the two PBZ domains from human APLF and their interaction with poly(ADP-ribose). Eustermann, S., Brockmann, C., Mehrotra, P.V. et al. Nat Struct Mol Biol (2010) 17:241-243. DOI 10.1038/nsmb.1747 · PubMed

Other PDB entries of the same protein (UniProt Q8IW19 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5W7W 1.35 Å, Crystal Structure of FHA domain of human APLF
5E50 1.38 Å, APLF/XRCC4 complex
6TYZ 1.51 Å, Structure of Ku80 von Willebrand domain complexed with APLF Ku Binding Motif
6TYW 1.7 Å, Structure of Ku80 von Willebrand domain S229A mutant complexed with APLF Ku Binding Motif
5W7X 2.0 Å, Crystal Structure of FHA domain of human APLF in complex with XRCC1 bisphospho peptide
5W7Y 2.1 Å, Crystal Structure of FHA domain of human APLF in complex with XRCC1 monophosphorylated…
6YN1 2.35 Å, Crystal structure of histone chaperone APLF acidic domain bound to the histone…
6TYT 2.4 Å, Structure of Ku80 von Willebrand domain S229A mutant complexed with APLF and XLF Ku…
6ERF 3.01 Å, Complex of APLF factor and Ku heterodimer bound to DNA
2KQB First PBZ domain of human APLF protein
2KQC Second PBZ domain of human APLF protein
2KQE Second PBZ domain of human APLF protein in complex with ribofuranosyladenosine

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