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Protein Structures and Oligomeric States

Enter a protein name, UniProt accession or PDB ID. Name searches ask you to confirm the protein identity before related structures are queried.

Current Protein Identity：Q8IW19 New Search
11PDB entries
23Biological assembly
27chain/assembly records
Main Difference Dimensions in This Set
Different construct Different mutation/modification Different assembly state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics

Difference tags compare only the current result set; every original PDB and assembly record remains separate.

Related-Structure Differences

Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.

PDB Entry Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Experimental Method Experimental Conditions Structure Quality
2KQB First PBZ domain of human APLF protein Deposited 2009-11-04 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 368–451（84 aa） Fragment：sequence database residues 363-451, PBZ-type 1 domain
Not recorded ZN ZINC ION × 1 SOLUTION NMR
NMR measurement conditions pH 6；300 K；Ionic strength (raw mmCIF value) 0.4；Pressure ambient
NMR sample composition 20 mM potassium pyrophosphate, 200 mM sodium chloride, 100 uM zinc sulphate, 2 mM [U-2H] DTT, 0.5-0.6 mM [U-98% 13C; U-98% 15N] APLF_363-451, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 20 mM potassium pyrophosphate, 200 mM sodium chloride, 100 uM zinc sulphate, 2 mM [U-2H] DTT, 0.5-0.6 mM [U-98% 13C; U-98% 15N] APLF_363-451, 100% D2O | 100% D2O
Resolution not provided
2KQC Second PBZ domain of human APLF protein Deposited 2009-11-04 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 368–451（84 aa） Fragment：sequence database residues 368-451, PBZ-type 2 domain
Not recorded ZN ZINC ION × 1 SOLUTION NMR
NMR measurement conditions pH 6；300 K；Ionic strength (raw mmCIF value) 0.4；Pressure ambient
NMR sample composition 20 mM potassium pyrophosphate, 200 mM sodium chloride, 100 uM zinc sulphate, 2 mM [U-2H] DTT, 0.5-0.6 mM [U-98% 13C; U-98% 15N] APLF_363-451, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 20 mM potassium pyrophosphate, 200 mM sodium chloride, 100 uM zinc sulphate, 2 mM [U-2H] DTT, 0.5-0.6 mM [U-98% 13C; U-98% 15N] APLF_363-451, 100% D2O | 100% D2O
Resolution not provided
2KQD First PBZ domain of human APLF protein in complex with ribofuranosyladenosine Deposited 2009-11-04 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 368–451（84 aa） Fragment：sequence database residues 363-451, PBZ-type 1 domain
Not recorded ZN ZINC ION × 1 ADN ADENOSINE × 1 RIB alpha-D-ribofuranose × 1 SOLUTION NMR
NMR measurement conditions pH 6；278 K；Ionic strength (raw mmCIF value) 0.4；Pressure ambient
NMR measurement conditions pH 6；286 K；Ionic strength (raw mmCIF value) 0.4；Pressure ambient
NMR measurement conditions pH 6；300 K；Ionic strength (raw mmCIF value) 0.4；Pressure ambient
NMR sample composition 20 mM potassium pyrophosphate, 200 mM sodium chloride, 100 uM zinc sulphate, 2 mM [U-2H] DTT, 0.8 mM [U-98% 13C; U-98% 15N] APLF_363-451, 2 mM RFA, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 20 mM potassium pyrophosphate, 200 mM sodium chloride, 100 uM zinc sulphate, 2 mM [U-2H] DTT, 0.8 mM [U-98% 13C; U-98% 15N] APLF_363-451, 2 mM RFA, 100% D2O | 100% D2O
Resolution not provided
2KQE Second PBZ domain of human APLF protein in complex with ribofuranosyladenosine Deposited 2009-11-04 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 368–451（84 aa） Fragment：sequence database residues 363-451, PBZ-type 2 domain
Not recorded ZN ZINC ION × 1 ADN ADENOSINE × 1 RIB alpha-D-ribofuranose × 1 SOLUTION NMR
NMR measurement conditions pH 6；278 K；Ionic strength (raw mmCIF value) 0.4；Pressure ambient
NMR measurement conditions pH 6；286 K；Ionic strength (raw mmCIF value) 0.4；Pressure ambient
NMR measurement conditions pH 6；300 K；Ionic strength (raw mmCIF value) 0.4；Pressure ambient
NMR sample composition 20 mM potassium pyrophosphate, 200 mM sodium chloride, 100 uM zinc sulphate, 2 mM [U-2H] DTT, 0.8 mM [U-98% 13C; U-98% 15N] APLF_363-451, 2 mM RFA, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 20 mM potassium pyrophosphate, 200 mM sodium chloride, 100 uM zinc sulphate, 2 mM [U-2H] DTT, 0.8 mM [U-98% 13C; U-98% 15N] APLF_363-451, 2 mM RFA, 100% D2O | 100% D2O
Resolution not provided
2KUO Structure and identification of ADP-ribose recognition motifs of APLF and role in the DNA damage response Deposited 2010-02-23 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 360–448（89 aa） Fragment：APLF TZF
Not recorded ZN ZINC ION × 2 SOLUTION NMR
NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 50；Pressure ambient
NMR measurement conditions pH 7.4；298 K；Ionic strength (raw mmCIF value) 150；Pressure ambient
NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 500；Pressure ambient
NMR sample composition 0.5-0.8 mM [U-100% 13C; U-100% 15N] APLF Tandem ZF, 20 mM Bis-tris, 50 mM sodium chloride, 1 mM sodium azide, 0.05 mM zinc chloride, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition 0.5-0.8 mM [U-100% 13C; U-100% 15N] APLF Tandem ZF, 20 mM Bis-tris, 50 mM sodium chloride, 1 mM sodium azide, 0.05 mM zinc chloride, 99% D2O | 99% D2O
NMR sample composition 0.1 mM [U-100% 15N] APLF Tandem ZF, 20 mM Bis-tris, 50 mM sodium chloride, 1 mM sodium azide, 0.05 mM zinc chloride, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition 0.1 mM [U-100% 15N] APLF Tandem ZF, 20 mM sodium phosphate, 150 mM potassium chloride, 1 mM sodium azide, 0.05 mM zinc chloride, 2 mM magnesium chloride, 93% H2O/7% D2O | 93% H2O/7% D2O
NMR sample composition 0.5 mM [U-100% 15N] APLF Tandem ZF, 20 mM Bis-tris, 500 mM sodium chloride, 1 mM sodium azide, 0.05 mM zinc chloride, 10 mg/mL Pf1 phage, 93% H2O/7% D2O | 93% H2O/7% D2O
Resolution not provided
5E50 APLF/XRCC4 complex Deposited 2015-10-07 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 1–105（105 aa）
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；Protein complex at 10 mg/ml, in 50 mM HEPES pH 7.5, 150 mM NaCl, 5 mM beta-mercaptoethanol. The complex crystallised from hanging drops set up at 18 oC with equal volumes of protein and reservoir solution 0.1M Tris pH 8.0, 30% w/v PEG 3350, 0.2M MgCl2.
Resolution 1.38 Å R-free 0.174
5E50 APLF/XRCC4 complex Deposited 2015-10-07 Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain B 1–105（105 aa）
Not recorded MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；Protein complex at 10 mg/ml, in 50 mM HEPES pH 7.5, 150 mM NaCl, 5 mM beta-mercaptoethanol. The complex crystallised from hanging drops set up at 18 oC with equal volumes of protein and reservoir solution 0.1M Tris pH 8.0, 30% w/v PEG 3350, 0.2M MgCl2.
Resolution 1.38 Å R-free 0.174
5W7W Crystal Structure of FHA domain of human APLF Deposited 2017-06-21 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain T 1–105（105 aa） Fragment：UNP residues 1-105
Not recorded FMT FORMIC ACID × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；3.5M sodium formate
Resolution 1.35 Å R-free 0.164
5W7W Crystal Structure of FHA domain of human APLF Deposited 2017-06-21 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1–105（105 aa） Fragment：UNP residues 1-105
Not recorded FMT FORMIC ACID × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；3.5M sodium formate
Resolution 1.35 Å R-free 0.164
5W7X Crystal Structure of FHA domain of human APLF in complex with XRCC1 bisphospho peptide Deposited 2017-06-21 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain D 1–105（105 aa） Fragment：UNP residues 1-105
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.6mM XRCC1 bisphosphopeptide 0.6mM APLF 0.5M lithium chloride 0.1M Tris 28% PEG 6000
Resolution 2.00 Å R-free 0.229
5W7X Crystal Structure of FHA domain of human APLF in complex with XRCC1 bisphospho peptide Deposited 2017-06-21 Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 1–105（105 aa） Fragment：UNP residues 1-105
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.6mM XRCC1 bisphosphopeptide 0.6mM APLF 0.5M lithium chloride 0.1M Tris 28% PEG 6000
Resolution 2.00 Å R-free 0.229
5W7X Crystal Structure of FHA domain of human APLF in complex with XRCC1 bisphospho peptide Deposited 2017-06-21 Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain B 1–105（105 aa） Fragment：UNP residues 1-105
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.6mM XRCC1 bisphosphopeptide 0.6mM APLF 0.5M lithium chloride 0.1M Tris 28% PEG 6000
Resolution 2.00 Å R-free 0.229
5W7X Crystal Structure of FHA domain of human APLF in complex with XRCC1 bisphospho peptide Deposited 2017-06-21 Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain C 1–105（105 aa） Fragment：UNP residues 1-105
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.6mM XRCC1 bisphosphopeptide 0.6mM APLF 0.5M lithium chloride 0.1M Tris 28% PEG 6000
Resolution 2.00 Å R-free 0.229
5W7Y Crystal Structure of FHA domain of human APLF in complex with XRCC1 monophosphorylated mutated peptide Deposited 2017-06-21 Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain A 1–105（105 aa） Fragment：UNP residues 1-105
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.6mM APLF 0.6mM XRCC1 peptide 0.1M Tris 30% PEG 1000
Resolution 2.10 Å R-free 0.237
5W7Y Crystal Structure of FHA domain of human APLF in complex with XRCC1 monophosphorylated mutated peptide Deposited 2017-06-21 Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count
Chain B 1–105（105 aa） Fragment：UNP residues 1-105
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.6mM APLF 0.6mM XRCC1 peptide 0.1M Tris 30% PEG 1000
Resolution 2.10 Å R-free 0.237
6ERF Complex of APLF factor and Ku heterodimer bound to DNA Deposited 2017-10-18 Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric（5） Consistent with all polymers
Chain Q 174–191（18 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；100 mM Bris Tris propane 13% PEG 3350 150 mM Na nirate
Resolution 3.01 Å R-free 0.227
6ERF Complex of APLF factor and Ku heterodimer bound to DNA Deposited 2017-10-18 Assembly 2 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric（5） Consistent with all polymers
Chain R 174–191（18 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；100 mM Bris Tris propane 13% PEG 3350 150 mM Na nirate
Resolution 3.01 Å R-free 0.227
6ERF Complex of APLF factor and Ku heterodimer bound to DNA Deposited 2017-10-18 Assembly 3 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric（5） Consistent with all polymers
Chain S 174–191（18 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；100 mM Bris Tris propane 13% PEG 3350 150 mM Na nirate
Resolution 3.01 Å R-free 0.227
6ERF Complex of APLF factor and Ku heterodimer bound to DNA Deposited 2017-10-18 Assembly 4 Protein–DNA Heteromer；Protein × 3 PDB declaration: pentameric（5） Consistent with all polymers
Chain T 174–191（18 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；100 mM Bris Tris propane 13% PEG 3350 150 mM Na nirate
Resolution 3.01 Å R-free 0.227
6YN1 Crystal structure of histone chaperone APLF acidic domain bound to the histone H2A-H2B-H3-H4 octamer Deposited 2020-04-10 Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric（10） Consistent with protein count
Chain E 449–490（42 aa）
Chain J 449–490（42 aa）
Not recorded GOL GLYCEROL × 3 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M sodium cacodylate pH6.5, 1.0 M tri-sodium citrate
Resolution 2.35 Å R-free 0.233
6YN1 Crystal structure of histone chaperone APLF acidic domain bound to the histone H2A-H2B-H3-H4 octamer Deposited 2020-04-10 Assembly 2 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric（10） Consistent with protein count
Chain O 449–490（42 aa）
Chain T 449–490（42 aa）
Not recorded GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M sodium cacodylate pH6.5, 1.0 M tri-sodium citrate
Resolution 2.35 Å R-free 0.233
6YN1 Crystal structure of histone chaperone APLF acidic domain bound to the histone H2A-H2B-H3-H4 octamer Deposited 2020-04-10 Assembly 3 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric（10） Consistent with protein count
Chain Y 449–490（42 aa）
Chain d 449–490（42 aa）
Not recorded GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M sodium cacodylate pH6.5, 1.0 M tri-sodium citrate
Resolution 2.35 Å R-free 0.233
6YN1 Crystal structure of histone chaperone APLF acidic domain bound to the histone H2A-H2B-H3-H4 octamer Deposited 2020-04-10 Assembly 4 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric（10） Consistent with protein count
Chain i 449–490（42 aa）
Chain n 449–490（42 aa）
Not recorded GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.1 M sodium cacodylate pH6.5, 1.0 M tri-sodium citrate
Resolution 2.35 Å R-free 0.233

This page presents structural evidence recorded in PDB/mmCIF.“No recorded non-water small molecule” does not prove that the experimental sample was ligand-free; experimental conditions belong to the PDB experiment, while ligands and copy counts are shown for each biological assembly.