SAXSdb — 2zne

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Programmed cell death protein 6

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 2–191	Fragment：residues 2-191	16-meric peptide from Programmed cell death 6-interacting protein × 1 （Q8WUM4） ZN ZINC ION × 4 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；10% 2-propanol, 0.1M Cacodylate, 0.2M zinc acetate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.20 Å R-free 0.274
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 2–191	Fragment：residues 2-191	16-meric peptide from Programmed cell death 6-interacting protein × 1 （Q8WUM4） ZN ZINC ION × 4 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；10% 2-propanol, 0.1M Cacodylate, 0.2M zinc acetate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.20 Å R-free 0.274
3	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 2–191 Chain B； UniProt 2–191	Fragment：residues 2-191	16-meric peptide from Programmed cell death 6-interacting protein × 2 （Q8WUM4） ZN ZINC ION × 8 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；10% 2-propanol, 0.1M Cacodylate, 0.2M zinc acetate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.20 Å R-free 0.274

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 2ZNE	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2ZN8 Crystal structure of Zn2+-bound form of ALG-2 Deposited 2008-04-22	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–191（190 aa）	Not recorded	ZN ZINC ION × 8 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；25% 2-methyl-2,4-pentanediol, 100mM Cacodylate, 75mM Zinc acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.70 Å R-free 0.260
2ZN9 Crystal structure of Ca2+-bound form of des3-20ALG-2 Deposited 2008-04-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 20–191（172 aa） Fragment：residues 20-191 Chain B 20–191（172 aa） Fragment：residues 20-191	Not recorded	CA CALCIUM ION × 7 2PE NONAETHYLENE GLYCOL × 1 12P DODECAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；18% PEG 8000, 0.1M Sodium Cacodylate, 0.2M Calcium Acetate hydrate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.40 Å R-free 0.298
2ZN9 Crystal structure of Ca2+-bound form of des3-20ALG-2 Deposited 2008-04-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 20–191（172 aa） Fragment：residues 20-191 Chain B 20–191（172 aa） Fragment：residues 20-191	Not recorded	CA CALCIUM ION × 7 2PE NONAETHYLENE GLYCOL × 1 12P DODECAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；18% PEG 8000, 0.1M Sodium Cacodylate, 0.2M Calcium Acetate hydrate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.40 Å R-free 0.298
2ZND Crystal structure of Ca2+-free form of des3-20ALG-2 Deposited 2008-04-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 20–191（172 aa） Fragment：residues 20-191	Not recorded	MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 10 PO4 PHOSPHATE ION × 4 NA SODIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；40% 2-methyl-2,4-pentanediol, 0.1M Na2HPO4-KH2PO4, 2mM EDTA, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.70 Å R-free 0.222
2ZRS Crystal structure of Ca2+-bound form of des3-23ALG-2 Deposited 2008-09-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 24–191（168 aa） Fragment：UNP residues 24-191 Chain B 24–191（168 aa） Fragment：UNP residues 24-191	Not recorded	CA CALCIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；50mM MES, 12.5% 2-propanol, 150mM calcium acetate, pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.10 Å R-free 0.280
2ZRS Crystal structure of Ca2+-bound form of des3-23ALG-2 Deposited 2008-09-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 24–191（168 aa） Fragment：UNP residues 24-191 Chain D 24–191（168 aa） Fragment：UNP residues 24-191	Not recorded	CA CALCIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；50mM MES, 12.5% 2-propanol, 150mM calcium acetate, pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.10 Å R-free 0.280
2ZRS Crystal structure of Ca2+-bound form of des3-23ALG-2 Deposited 2008-09-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 24–191（168 aa） Fragment：UNP residues 24-191 Chain F 24–191（168 aa） Fragment：UNP residues 24-191	Not recorded	CA CALCIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；50mM MES, 12.5% 2-propanol, 150mM calcium acetate, pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.10 Å R-free 0.280
2ZRS Crystal structure of Ca2+-bound form of des3-23ALG-2 Deposited 2008-09-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain G 24–191（168 aa） Fragment：UNP residues 24-191 Chain H 24–191（168 aa） Fragment：UNP residues 24-191	Not recorded	CA CALCIUM ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；50mM MES, 12.5% 2-propanol, 150mM calcium acetate, pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.10 Å R-free 0.280
2ZRT Crystal structure of Zn2+-bound form of des3-23ALG-2 Deposited 2008-09-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 24–191（168 aa） Fragment：UNP residues 24-191 Chain B 24–191（168 aa） Fragment：UNP residues 24-191	Not recorded	ZN ZINC ION × 9	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；100mM MES, 15% ethanol, 200mM zinc acetate, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.30 Å R-free 0.221
2ZRT Crystal structure of Zn2+-bound form of des3-23ALG-2 Deposited 2008-09-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 24–191（168 aa） Fragment：UNP residues 24-191 Chain D 24–191（168 aa） Fragment：UNP residues 24-191	Not recorded	ZN ZINC ION × 11	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；100mM MES, 15% ethanol, 200mM zinc acetate, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.30 Å R-free 0.221
2ZRT Crystal structure of Zn2+-bound form of des3-23ALG-2 Deposited 2008-09-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 24–191（168 aa） Fragment：UNP residues 24-191 Chain F 24–191（168 aa） Fragment：UNP residues 24-191	Not recorded	ZN ZINC ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；100mM MES, 15% ethanol, 200mM zinc acetate, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.30 Å R-free 0.221
2ZRT Crystal structure of Zn2+-bound form of des3-23ALG-2 Deposited 2008-09-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain G 24–191（168 aa） Fragment：UNP residues 24-191 Chain H 24–191（168 aa） Fragment：UNP residues 24-191	Not recorded	ZN ZINC ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；100mM MES, 15% ethanol, 200mM zinc acetate, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.30 Å R-free 0.221
3AAJ Crystal structure of Ca2+-bound form of des3-23ALG-2deltaGF122 Deposited 2009-11-19	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–191（190 aa） Fragment：residues 2-191 Chain B 2–191（190 aa） Fragment：residues 2-191	Mutation：deletions of residues 3-23, G121, F122 Mutation：deletions of residues 3-23, G121, F122	CA CALCIUM ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.05M Cacodylate, 2.5% PEG 4000, 0.3M Ammonium acetate, 0.01M CaCl2, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.266
3AAK Crystal structure of Zn2+-bound form of des3-20ALG-2F122A Deposited 2009-11-19	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–191（190 aa） Fragment：residues 2-191	Mutation：deletions of residues 3-20, F122A	ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；25% 2-methyl-2,4-pentanediol, 100mM Cacodylate, 50mM Zinc acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.70 Å R-free 0.298
3WXA X-ray crystal structural analysis of the complex between ALG-2 and Sec31A peptide Deposited 2014-07-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 20–191（172 aa） Fragment：UNP residues 20-191	Not recorded	ZN ZINC ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.1M Cacodylate, 20% MPD, 0.05M Zinc Acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.36 Å R-free 0.263
3WXA X-ray crystal structural analysis of the complex between ALG-2 and Sec31A peptide Deposited 2014-07-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 20–191（172 aa） Fragment：UNP residues 20-191	Not recorded	ZN ZINC ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.1M Cacodylate, 20% MPD, 0.05M Zinc Acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.36 Å R-free 0.263
5GQQ Structure of ALG-2/HEBP2 Complex Deposited 2016-08-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 24–191（168 aa） Fragment：UNP RESIDUES 24-191 Chain D 24–191（168 aa） Fragment：UNP RESIDUES 24-191	Not recorded	CA CALCIUM ION × 6 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；293.15 K；0.1 M Bis-Tris, 2 M NaCl, pH 5.5	Resolution 2.20 Å R-free 0.225

9 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PDCD6_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–169； UniProt 2–191 Author chain B； PDBConstruct 1–169； UniProt 2–191

16-meric peptide from Programmed cell death 6-interacting protein

OrganismNot specified

UniProt Q8WUM4

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 799–814	Fragment：ALG-2 binding site, residues 799-814 Mutation：C15S	Programmed cell death protein 6 × 1 （O75340） ZN ZINC ION × 4 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；10% 2-propanol, 0.1M Cacodylate, 0.2M zinc acetate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.20 Å R-free 0.274
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 799–814	Fragment：ALG-2 binding site, residues 799-814 Mutation：C15S	Programmed cell death protein 6 × 1 （O75340） ZN ZINC ION × 4 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；10% 2-propanol, 0.1M Cacodylate, 0.2M zinc acetate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.20 Å R-free 0.274
3	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain C； UniProt 799–814 Chain D； UniProt 799–814	Fragment：ALG-2 binding site, residues 799-814 Mutation：C15S	Programmed cell death protein 6 × 2 （O75340） ZN ZINC ION × 8 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；10% 2-propanol, 0.1M Cacodylate, 0.2M zinc acetate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.20 Å R-free 0.274

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 2ZNE	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2OEV Crystal structure of ALIX/AIP1 Deposited 2007-01-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–698（698 aa） Fragment：Bro1-V Domains, residues 1-698	Mutation：K268Y, K269Y	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；286 K；8% PEG 4000, 0.1M ammonium acetate, 0.1M magnesium acetate, 0.05M hepes, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 286K	Resolution 3.30 Å R-free 0.317
2OEW Structure of ALIX/AIP1 Bro1 Domain Deposited 2007-01-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–359（359 aa） Fragment：Bro1 Domain, residues 1-359	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；286 K；10% PEG 20000, 0.1M NaMES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 286K	Resolution 2.55 Å R-free 0.274
2OEX Structure of ALIX/AIP1 V Domain Deposited 2007-01-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 360–702（343 aa） Fragment：V Domain, residues 359-702 Chain B 360–702（343 aa） Fragment：V Domain, residues 359-702	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；277 K；14% PEG 3350, 0.16M magnesium formate, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.58 Å R-free 0.302
2OJQ Crystal structure of Alix V domain Deposited 2007-01-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 360–702（343 aa） Fragment：V domain, residues 360-702	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；13-15% PEG 6000, 6-10% ethylene glycol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 100K	Resolution 2.87 Å R-free 0.318
2R02 Crystal Structure of ALIX/AIP1 in complex with the HIV-1 YPLTSL Late Domain Deposited 2007-08-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–698（697 aa） Fragment：ALIX Bro1-V domains	Mutation：K268Y,K269Y	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions sitting drop vapor diffusion；pH 5.9；286 K；0.20-0.25 M MgCl2, 7-10% PEG 4000, 0.1 M NaMES, pH 5.9, sitting drop vapor diffusion, temperature 286K	Resolution 2.60 Å R-free 0.285
2R03 Crystal Structure of ALIX/AIP1 in complex with the YPDL Late Domain Deposited 2007-08-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–698（697 aa） Fragment：ALIX Bro1-V domains	Mutation：K268Y,K269Y	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.9；286 K；0.20-0.25 M MgCl2, 7-10% PEG 4000, 0.1 M NaMES, pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 286K	Resolution 2.59 Å R-free 0.286
2R05 Crystal Structure of ALIX/AIP1 in complex with the HIV-1 YPLASL Late Domain Deposited 2007-08-17	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–698（697 aa） Fragment：ALIX Bro1-V domains	Mutation：K268Y,K269Y	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.9；286 K；0.20-0.25 M MgCl2, 7-10% PEG 4000, 0.1 M NaMES, pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 286K	Resolution 2.55 Å R-free 0.280
2XS1 Crystal Structure of ALIX in complex with the SIVmac239 PYKEVTEDL Late Domain Deposited 2010-09-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–698（698 aa） Fragment：BRO1-V DOMAINS, RESIDUES 1-698	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.2；6.5% PEG4000, 0.2 MGCL2, 0.1M MES PH 6.2	Resolution 2.30 Å R-free 0.252
2XS8 Crystal Structure of ALIX in complex with the SIVagmTan-1 AYDPARKLL Late Domain Deposited 2010-09-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–698（698 aa） Fragment：BRO1-V DOMAINS, RESIDUES 1-698	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.1；6.1% PEG4000, 0.2M MGCL2, 0.1M MES PH 6.1	Resolution 2.50 Å R-free 0.261
3C3O ALIX Bro1-domain:CHMIP4A co-crystal structure Deposited 2008-01-28	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–359（359 aa） Fragment：BRO1 domain (UNP residues 1-358)	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；15% PEG 8,000, 100mM Na MES pH 6.5, 200mM Na Acetate, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.15 Å R-free 0.284
3C3Q ALIX Bro1-domain:CHMIP4B co-crystal structure Deposited 2008-01-28	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–359（359 aa） Fragment：BRO1 domain (UNP residues 1-359)	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；15% PEG 8,000, 100mM Na MES pH 6.5, 200mM Na Acetate, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.10 Å R-free 0.290
3C3R ALIX BRO1 CHMP4C complex Deposited 2008-01-28	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–359（359 aa） Fragment：BRO1 domain (UNP residues 1-359)	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；10% PEG 2,000, 100mM Na MES pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.02 Å R-free 0.288
3E1R Midbody targeting of the ESCRT machinery by a non-canonical coiled-coil in CEP55 Deposited 2008-08-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 797–809（13 aa） Fragment：UNP residues 797-809	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；294 K；100 mM MES, 22% PEG 6000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.00 Å R-free 0.248
3WUV Structure basis of inactivating cell abscission with chimera peptide 2 Deposited 2014-05-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 796–809（14 aa）	Mutation：P796D/P807I/G808P/Y809P	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；295 K；0.8M ammonium sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.79 Å R-free 0.227
3WUV Structure basis of inactivating cell abscission with chimera peptide 2 Deposited 2014-05-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 796–809（14 aa）	Mutation：P796D/P807I/G808P/Y809P	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；295 K；0.8M ammonium sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.79 Å R-free 0.227
3WUV Structure basis of inactivating cell abscission with chimera peptide 2 Deposited 2014-05-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 796–809（14 aa）	Mutation：P796D/P807I/G808P/Y809P	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；295 K；0.8M ammonium sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.79 Å R-free 0.227
3WUV Structure basis of inactivating cell abscission with chimera peptide 2 Deposited 2014-05-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain L 796–809（14 aa）	Mutation：P796D/P807I/G808P/Y809P	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；295 K；0.8M ammonium sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.79 Å R-free 0.227
3WUV Structure basis of inactivating cell abscission with chimera peptide 2 Deposited 2014-05-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain O 796–809（14 aa）	Mutation：P796D/P807I/G808P/Y809P	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；295 K；0.8M ammonium sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.79 Å R-free 0.227
3WUV Structure basis of inactivating cell abscission with chimera peptide 2 Deposited 2014-05-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain R 796–809（14 aa）	Mutation：P796D/P807I/G808P/Y809P	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；295 K；0.8M ammonium sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.79 Å R-free 0.227
4JJY Alix V domain Deposited 2013-03-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 355–708（354 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；0.1 M sodium citrate pH 5, 6-8% PEG 8000, 5-10% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 6.50 Å R-free 0.283
4JJY Alix V domain Deposited 2013-03-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 355–708（354 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；0.1 M sodium citrate pH 5, 6-8% PEG 8000, 5-10% ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 6.50 Å R-free 0.283
5V3R CHMP4C in complex with ALIX BRO1 Deposited 2017-03-08	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–359（359 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293.15 K；10% PEG20000, 100 mM MES, pH 6.5	Resolution 1.91 Å R-free 0.213
5WA1 CHMP4C A232T in complex with ALIX BRO1 Deposited 2017-06-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–358（358 aa） Fragment：Bro1 domain (UNP residues 1-358)	Mutation：A232T	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293.15 K；15% PEG8000, 100 mM MES, pH 6.5, 200 mM sodium acetate	Resolution 1.87 Å R-free 0.215
6KP3 STRUCTURE OF SENDAI VIRUS Y3/ALIX-BRO1 DOMAIN COMPLEX Deposited 2019-08-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–359（359 aa） Fragment：bro1 domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.45；297 K；15% PEG 3350, 0.2M Sodium Malonate-NaOH	Resolution 2.20 Å R-free 0.262

18 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PDC6I_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–16； UniProt 799–814 Author chain D； PDBConstruct 1–16； UniProt 799–814

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2zne
Deposition date deposition_date	2008-04-22
Structure title title	Crystal structure of Zn2+-bound form of des3-23ALG-2 complexed with Alix ABS peptide
Keywords keywords	;PENTA-EF-HAND PROTEIN, CALCIUM BINDING PROTEIN, Apoptosis, Endoplasmic reticulum, Membrane, Nucleus, Polymorphism, Cytoplasm, Host-virus interaction, Protein transport, Transport ;; APOPTOSIS
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	25.93 Å
Radius of gyration Rg (electron density) rg_electron	24.68 Å
Forward intensity I(0) i0	31930700.00
Molecular weight molecular_weight	42931.0 kDa
Excluded volume excluded_volume	53214 Å³
Envelope volume envelope_volume	66407 Å³
Hydration-shell volume shell_volume	22869 Å³
Envelope diameter envelope_diameter	82.5 Å
Shell Rg shell_rg	31.24 Å
Envelope Rg envelope_rg	24.29 Å
Shape Rg shape_rg	24.67 Å
Total Rg total_rg	25.47 Å
Total atoms total_atoms	3012
Residues n_residues	362
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	80.4 Å
Rg (real space) rg_real	25.84 Å
Rg uncertainty (real space) rg_real_error	0.52 Å
I(0) (real space) i0_real	3.1930e+07
I(0) uncertainty (real space) i0_real_error	3.9580e+05
Rg (reciprocal space) rg_reciprocal	25.87 Å
I(0) (reciprocal space) i0_reciprocal	31930000.0000
Solution quality estimate total_estimate	0.9130
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	36.9 Å
Skewness Skewness skewness	0.104
Kurtosis Kurtosis kurtosis	-0.686
Angular range angular_range	— – 0.3050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4531000.0000
Real-space data points n_real_points	62
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.960; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.991

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Programmed cell death protein 6
Molecular weight formula_weight	19877.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3080

ADQSFLWNVFQRVDKDRSGVISDTELQQALSNGTWTPFNPVTVRSIISMFDRENKAGVNFSEFTGVWKYITDWQNVFRTYDRDNSGMIDKNELKQALSGFGYRLSDQFHDILIRKFDRQGRGQIAFDDFIQGCIVLQRLTDIFRRYDTDQDGWIQVSYEQYLSMVFSIV

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	16-meric peptide from Programmed cell death 6-interacting protein
Molecular weight formula_weight	1771.9 kDa
Mutation mutation	C15S
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

QGPPYPTYPGYPGYSQ

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	68

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	2zneA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

Domain ID domain_id	2zneB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

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8. Citations (1)

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Unit-cell length a length_a	47.449 Å
Unit-cell length b length_b	88.509 Å
Unit-cell length c length_c	211.556 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	33.940 Å
R factor r_factor	0.2255
R_work r_work	0.2228
R_free r_free	0.2739

fit	/app/data/saxs_computation/zn/2zne/2zne.fit
pddf	/app/data/pr_computation/zn/2zne/2zne.pr.out
profile	/app/data/saxs_computation/zn/2zne/2zne.dat

Crystal structure of Zn2+-bound form of des3-23ALG-2 complexed with Alix ABS peptide

1. Protein Identity and Related Structures Protein Identity & Related Structures

Programmed cell death protein 6

State in the Current Structure

Other States of the Same Protein in the Database

16-meric peptide from Programmed cell death 6-interacting protein

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)