1dfn

CRYSTAL STRUCTURE OF DEFENSIN HNP-3, AN AMPHIPHILIC DIMER: MECHANISMS OF MEMBRANE PERMEABILIZATION

Method: X-RAY DIFFRACTION D_max: 38.3 Å Quality: GOOD

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

DEFENSIN HNP-3

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 66–94 Chain B； UniProt 66–94	Not recorded	No other associated polymer	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.90 Å
2	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 66–94 Chain B； UniProt 66–94	Not recorded	No other associated polymer	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.90 Å

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 1DFN	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2KHT NMR Structure of human alpha defensin HNP-1 Deposited 2009-04-11	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 65–94（30 aa） Fragment：Residues 65-94	Not recorded	No recorded non-water small molecule	SOLID-STATE NMR NMR measurement conditions pH 6.5；268 K；Pressure 1 NMR measurement conditions pH 6.5；253 K；Pressure 1 NMR sample composition Polycrystalline sample grown from 60% w/v PEG400, 30 mM Cacodylate, 60 mM Lithium Sulfate	Resolution not provided
2PM1 Derivative of human alpha-defensin 1 (HNP1) Deposited 2007-04-20	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 65–94（30 aa）	Mutation：Arg14->Dab, Arg15->Dab, Arg24->Dab 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 7.5；293 K；0.2 M sodium citrate, 0.1 M HEPES, 20 (v/v/) iso-Propanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.60 Å R-free 0.201
2PM4 Human alpha-defensin 1 (multiple Arg->Lys mutant) Deposited 2007-04-20	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 65–94（30 aa）	Mutation：Arg14->Lys, Arg15->Lys, Arg24->Lys	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.4 M ammonium phosphate monobasic, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.95 Å R-free 0.249
2PM4 Human alpha-defensin 1 (multiple Arg->Lys mutant) Deposited 2007-04-20	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 65–94（30 aa）	Mutation：Arg14->Lys, Arg15->Lys, Arg24->Lys	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.4 M ammonium phosphate monobasic, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.95 Å R-free 0.249
2PM5 Human alpha-defensin 1 derivative (HNP1) Deposited 2007-04-20	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 65–94（30 aa）	Mutation：Arg14->Orn, Arg15->Orn, Arg24->Orn Non-standard monomer：Yes (specific site not provided by mmCIF)	PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；0.1 M sodium citrate tribasic dihydrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.218
2PM5 Human alpha-defensin 1 derivative (HNP1) Deposited 2007-04-20	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 65–94（30 aa）	Mutation：Arg14->Orn, Arg15->Orn, Arg24->Orn 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 5.6；293 K；0.1 M sodium citrate tribasic dihydrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.218
2PM5 Human alpha-defensin 1 derivative (HNP1) Deposited 2007-04-20	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain B 65–94（30 aa）	Mutation：Arg14->Orn, Arg15->Orn, Arg24->Orn 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 5.6；293 K；0.1 M sodium citrate tribasic dihydrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.218
2PM5 Human alpha-defensin 1 derivative (HNP1) Deposited 2007-04-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 65–94（30 aa）	Mutation：Arg14->Orn, Arg15->Orn, Arg24->Orn Non-standard monomer：Yes (specific site not provided by mmCIF)	PO4 PHOSPHATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；0.1 M sodium citrate tribasic dihydrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.218
2PM5 Human alpha-defensin 1 derivative (HNP1) Deposited 2007-04-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 65–94（30 aa）	Mutation：Arg14->Orn, Arg15->Orn, Arg24->Orn Non-standard monomer：Yes (specific site not provided by mmCIF)	PO4 PHOSPHATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；0.1 M sodium citrate tribasic dihydrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.218
2PM5 Human alpha-defensin 1 derivative (HNP1) Deposited 2007-04-20	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 6 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 65–94（30 aa）	Mutation：Arg14->Orn, Arg15->Orn, Arg24->Orn 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 5.6；293 K；0.1 M sodium citrate tribasic dihydrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.218
3GNY Crystal structure of human alpha-defensin 1 (HNP1) Deposited 2009-03-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 65–94（30 aa） Chain B 65–94（30 aa）	Not recorded	CL CHLORIDE ION × 2 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1 M imidazole, pH 6.5, 1.0 M sodium acetate trihydrate, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.56 Å R-free 0.195
3GNY Crystal structure of human alpha-defensin 1 (HNP1) Deposited 2009-03-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 65–94（30 aa） Chain B 65–94（30 aa）	Not recorded	CL CHLORIDE ION × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1 M imidazole, pH 6.5, 1.0 M sodium acetate trihydrate, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.56 Å R-free 0.195
3H6C Crystal structure of human alpha-defensin 1 (Mutant Gln22Ala) Deposited 2009-04-23	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 65–94（30 aa） Chain B 65–94（30 aa）	Mutation：Q22A Mutation：Q22A	PEG DI(HYDROXYETHYL)ETHER × 4 CL CHLORIDE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.2 M magnesium acetate tetrahydrate, 0.1 M cacodylate trihydrate pH 6.5, 30% PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.63 Å R-free 0.199
3HJ2 Crystal structure of covalent dimer of HNP1 Deposited 2009-05-20	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 65–94（30 aa） Fragment：Residues 65-94 Chain B 65–94（30 aa） Fragment：Residues 65-94	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；293 K；0.1 M Na-citrate (pH 5.6), 0.2 M NH4-acetate, 30% (v/v) MPD, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 1.40 Å R-free 0.236
3HJD X-ray structure of monomeric variant of HNP1 Deposited 2009-05-21	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 65–94（30 aa） Fragment：Residues 65-94	Mutation：ILE84IML 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 7.5；293 K；0.1 M HEPES-Na (pH 7.5), 0.2 M sodium citrate, 30% (v/v) MPD, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 1.65 Å R-free 0.203
3HJD X-ray structure of monomeric variant of HNP1 Deposited 2009-05-21	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 65–94（30 aa） Fragment：Residues 65-94	Mutation：ILE84IML 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 7.5；293 K；0.1 M HEPES-Na (pH 7.5), 0.2 M sodium citrate, 30% (v/v) MPD, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 1.65 Å R-free 0.203
3LO1 Crystal structure of human alpha-defensin 1 (Y16A mutant) Deposited 2010-02-03	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 65–94（30 aa） Fragment：UNP residues 65-94	Mutation：Y16A	PG0 2-(2-METHOXYETHOXY)ETHANOL × 1 AZI AZIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；25% PEG 4,000; 0.2 M ammonium sulfate; 0.1 M sodium acetate, pH 4.6 , VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.60 Å R-free 0.225
3LO2 Crystal structure of human alpha-defensin 1 (Y21A mutant) Deposited 2010-02-03	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 65–94（30 aa） Fragment：UNP residues 65-94	Mutation：Y21A	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 TFA trifluoroacetic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；30% PEG 8,000; 0.2 M ammonium sulfate, pH pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.56 Å R-free 0.200
3LO2 Crystal structure of human alpha-defensin 1 (Y21A mutant) Deposited 2010-02-03	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 65–94（30 aa） Fragment：UNP residues 65-94	Mutation：Y21A	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；30% PEG 8,000; 0.2 M ammonium sulfate, pH pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.56 Å R-free 0.200
3LO2 Crystal structure of human alpha-defensin 1 (Y21A mutant) Deposited 2010-02-03	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 65–94（30 aa） Fragment：UNP residues 65-94 Chain B 65–94（30 aa） Fragment：UNP residues 65-94	Mutation：Y21A Mutation：Y21A	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 TFA trifluoroacetic acid × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；30% PEG 8,000; 0.2 M ammonium sulfate, pH pH 8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.56 Å R-free 0.200
3LO4 Crystal structure of human alpha-defensin 1 (R24A mutant) Deposited 2010-02-03	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 65–94（30 aa） Fragment：UNP residues 65-94	Mutation：R24A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；298 K；20% PEG 4,000; 0.1 M sodium citrate tribasic dehydrate; 20% iso-propanol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.75 Å R-free 0.210
3LO4 Crystal structure of human alpha-defensin 1 (R24A mutant) Deposited 2010-02-03	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 65–94（30 aa） Fragment：UNP residues 65-94	Mutation：R24A	PEG DI(HYDROXYETHYL)ETHER × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；298 K；20% PEG 4,000; 0.1 M sodium citrate tribasic dehydrate; 20% iso-propanol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.75 Å R-free 0.210
3LO4 Crystal structure of human alpha-defensin 1 (R24A mutant) Deposited 2010-02-03	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 65–94（30 aa） Fragment：UNP residues 65-94 Chain B 65–94（30 aa） Fragment：UNP residues 65-94	Mutation：R24A Mutation：R24A	PEG DI(HYDROXYETHYL)ETHER × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；298 K；20% PEG 4,000; 0.1 M sodium citrate tribasic dehydrate; 20% iso-propanol, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.75 Å R-free 0.210
3LO6 Crystal structure of human alpha-defensin 1 (W26Aba mutant) Deposited 2010-02-03	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 65–94（30 aa） Fragment：UNP residues 65-94	Mutation：W26Aba 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 7.5；298 K；30% MPD; 0.1 M HEPES sodium pH 7.5; 0.2 M sodium citrate dihydrate , VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.56 Å R-free 0.198
3LO6 Crystal structure of human alpha-defensin 1 (W26Aba mutant) Deposited 2010-02-03	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 65–94（30 aa） Fragment：UNP residues 65-94	Mutation：W26Aba Non-standard monomer：Yes (specific site not provided by mmCIF)	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；30% MPD; 0.1 M HEPES sodium pH 7.5; 0.2 M sodium citrate dihydrate , VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.56 Å R-free 0.198
3LO6 Crystal structure of human alpha-defensin 1 (W26Aba mutant) Deposited 2010-02-03	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 65–94（30 aa） Fragment：UNP residues 65-94 Chain B 65–94（30 aa） Fragment：UNP residues 65-94	Mutation：W26Aba Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：W26Aba Non-standard monomer：Yes (specific site not provided by mmCIF)	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；30% MPD; 0.1 M HEPES sodium pH 7.5; 0.2 M sodium citrate dihydrate , VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.56 Å R-free 0.198
3LO9 Crystal structure of human alpha-defensin 1 (W26Ahp mutant) Deposited 2010-02-03	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 65–94（30 aa） Fragment：UNP residues 65-94	Mutation：W26Ahp 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 6.5；298 K；0.1 M sodium cacodylate trihydrate pH 6.5; 0.2 M sodium citrate tribasic dehydrate; 30% isopropanol , VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.56 Å R-free 0.208
3LO9 Crystal structure of human alpha-defensin 1 (W26Ahp mutant) Deposited 2010-02-03	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 65–94（30 aa） Fragment：UNP residues 65-94	Mutation：W26Ahp 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 6.5；298 K；0.1 M sodium cacodylate trihydrate pH 6.5; 0.2 M sodium citrate tribasic dehydrate; 30% isopropanol , VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.56 Å R-free 0.208
3LO9 Crystal structure of human alpha-defensin 1 (W26Ahp mutant) Deposited 2010-02-03	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 65–94（30 aa） Fragment：UNP residues 65-94 Chain B 65–94（30 aa） Fragment：UNP residues 65-94	Mutation：W26Ahp Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：W26Ahp 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 6.5；298 K；0.1 M sodium cacodylate trihydrate pH 6.5; 0.2 M sodium citrate tribasic dehydrate; 30% isopropanol , VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.56 Å R-free 0.208
3LOE Crystal structure of human alpha-defensin 1 (F28A mutant) Deposited 2010-02-03	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 65–94（30 aa） Fragment：UNP residues 65-94	Mutation：F28A	SO4 SULFATE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；25% PEG 4,000; 0.2 M ammonium sulfate; 0.1 M sodium acetate, pH 4.6 , VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.56 Å R-free 0.184
3LOE Crystal structure of human alpha-defensin 1 (F28A mutant) Deposited 2010-02-03	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 65–94（30 aa） Fragment：UNP residues 65-94	Mutation：F28A	SO4 SULFATE ION × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；25% PEG 4,000; 0.2 M ammonium sulfate; 0.1 M sodium acetate, pH 4.6 , VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.56 Å R-free 0.184
3LVX Crystal structure of human alpha-defensin 1 (I6A mutant) Deposited 2010-02-22	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 65–94（30 aa） Fragment：HUMAN NEUTROPHIL DEFENSIN 1	Mutation：I6A	SO4 SULFATE ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；2% PEG 400; 0.1 M HEPES-Na, pH 7.5; 2 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.63 Å R-free 0.174
3LVX Crystal structure of human alpha-defensin 1 (I6A mutant) Deposited 2010-02-22	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 65–94（30 aa） Fragment：HUMAN NEUTROPHIL DEFENSIN 1	Mutation：I6A	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；2% PEG 400; 0.1 M HEPES-Na, pH 7.5; 2 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.63 Å R-free 0.174
3LVX Crystal structure of human alpha-defensin 1 (I6A mutant) Deposited 2010-02-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 48 PDB declaration: 48-meric	Chain A 65–94（30 aa） Fragment：HUMAN NEUTROPHIL DEFENSIN 1 Chain B 65–94（30 aa） Fragment：HUMAN NEUTROPHIL DEFENSIN 1	Mutation：I6A Mutation：I6A	SO4 SULFATE ION × 48 GOL GLYCEROL × 24	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；2% PEG 400; 0.1 M HEPES-Na, pH 7.5; 2 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.63 Å R-free 0.174
4DU0 Crystal structure of human alpha-defensin 1, HNP1 (G17A mutant) Deposited 2012-02-21	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 65–94（30 aa） Fragment：UNP residues 65-94	Mutation：G81A	GOL GLYCEROL × 1 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.2 Magnesium Chloride, 0.1M HEPES, pH7.5, 30% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.90 Å R-free 0.212
4DU0 Crystal structure of human alpha-defensin 1, HNP1 (G17A mutant) Deposited 2012-02-21	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 65–94（30 aa） Fragment：UNP residues 65-94	Mutation：G81A	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.2 Magnesium Chloride, 0.1M HEPES, pH7.5, 30% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.90 Å R-free 0.212
4DU0 Crystal structure of human alpha-defensin 1, HNP1 (G17A mutant) Deposited 2012-02-21	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 65–94（30 aa） Fragment：UNP residues 65-94	Mutation：G81A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.2 Magnesium Chloride, 0.1M HEPES, pH7.5, 30% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.90 Å R-free 0.212
4DU0 Crystal structure of human alpha-defensin 1, HNP1 (G17A mutant) Deposited 2012-02-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 65–94（30 aa） Fragment：UNP residues 65-94	Mutation：G81A	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.2 Magnesium Chloride, 0.1M HEPES, pH7.5, 30% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.90 Å R-free 0.212
4DU0 Crystal structure of human alpha-defensin 1, HNP1 (G17A mutant) Deposited 2012-02-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 65–94（30 aa） Fragment：UNP residues 65-94 Chain D 65–94（30 aa） Fragment：UNP residues 65-94	Mutation：G81A Mutation：G81A	GOL GLYCEROL × 2 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.2 Magnesium Chloride, 0.1M HEPES, pH7.5, 30% isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.90 Å R-free 0.212
4LB1 Crystal structure of human alpha-defensin 1 (HNP1) Y16A/F28A mutant Deposited 2013-06-20	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 65–94（30 aa） Chain B 65–94（30 aa） Chain D 65–94（30 aa） Chain E 65–94（30 aa）	Mutation：Y16A, F28A Mutation：Y16A, F28A Mutation：Y16A, F28A Mutation：Y16A, F28A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；2 M ammonium phosphate monobasic, 0.1 M Tris-HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.00 Å R-free 0.228
4LB7 Crystal structure of human alpha-defensin 1 (HNP1) Y16A/I20A/L25A/F28A mutant. Deposited 2013-06-20	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 65–94（30 aa） Chain B 65–94（30 aa） Chain D 65–94（30 aa） Chain E 65–94（30 aa）	Mutation：Y16A, I20A, L25A, F28A Mutation：Y16A, I20A, L25A, F28A Mutation：Y16A, I20A, L25A, F28A Mutation：Y16A, I20A, L25A, F28A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.8 M sodium phosphate monobasic, 0.8 M potassium phosphate monobasic, 0.1 M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.90 Å R-free 0.236
4LBB Crystal structure of human alpha-defensin 1 (HNP1) I20A mutant Deposited 2013-06-20	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 65–94（30 aa）	Mutation：I20A	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；30% PEG 4000, 0.1 M Tris-HCl pH 8.5, 0.2 M lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.72 Å R-free 0.229
4LBB Crystal structure of human alpha-defensin 1 (HNP1) I20A mutant Deposited 2013-06-20	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 65–94（30 aa）	Mutation：I20A	CL CHLORIDE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；30% PEG 4000, 0.1 M Tris-HCl pH 8.5, 0.2 M lithium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.72 Å R-free 0.229
4LBF Crystal structure of HUMAN ALPHA-DEFENSIN 1 (HNP1) I20A/L25A mutant Deposited 2013-06-20	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 65–94（30 aa） Chain B 65–94（30 aa） Chain C 65–94（30 aa） Chain D 65–94（30 aa）	Mutation：I20A, L25A Mutation：I20A, L25A Mutation：I20A, L25A Mutation：I20A, L25A	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；2 M ammonium sulfate, 0.1 M Tris-HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.70 Å R-free 0.231
4LBF Crystal structure of HUMAN ALPHA-DEFENSIN 1 (HNP1) I20A/L25A mutant Deposited 2013-06-20	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain E 65–94（30 aa） Chain F 65–94（30 aa） Chain G 65–94（30 aa） Chain H 65–94（30 aa）	Mutation：I20A, L25A Mutation：I20A, L25A Mutation：I20A, L25A Mutation：I20A, L25A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；2 M ammonium sulfate, 0.1 M Tris-HCl pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.70 Å R-free 0.231
9FQB crystal structure of ClY21-HNP1 Deposited 2024-06-14	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 65–94（30 aa） Chain B 65–94（30 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	ACT ACETATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M imidazole, 1.0 M sodium acetate, pH 6.5	Resolution 1.09 Å R-free 0.122

21 other PDB entries and 46 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DEF1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–30； UniProt 66–94 Author chain B； PDBConstruct 2–30； UniProt 66–94

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1dfn
Deposition date deposition_date	1991-01-18
Structure title title	CRYSTAL STRUCTURE OF DEFENSIN HNP-3, AN AMPHIPHILIC DIMER: MECHANISMS OF MEMBRANE PERMEABILIZATION
Keywords keywords	DEFENSIN; DEFENSIN
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	11.87 Å
Radius of gyration Rg (electron density) rg_electron	10.78 Å
Forward intensity I(0) i0	1185720.00
Molecular weight molecular_weight	6810.0 kDa
Excluded volume excluded_volume	8355 Å³
Envelope volume envelope_volume	9263 Å³
Hydration-shell volume shell_volume	7607 Å³
Envelope diameter envelope_diameter	37.0 Å
Shell Rg shell_rg	15.92 Å
Envelope Rg envelope_rg	11.18 Å
Shape Rg shape_rg	10.81 Å
Total Rg total_rg	12.14 Å
Total atoms total_atoms	470
Residues n_residues	60
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	38.3 Å
Rg (real space) rg_real	11.82 Å
Rg uncertainty (real space) rg_real_error	0.20 Å
I(0) (real space) i0_real	1.1860e+06
I(0) uncertainty (real space) i0_real_error	1.1060e+04
Rg (reciprocal space) rg_reciprocal	11.82 Å
I(0) (reciprocal space) i0_reciprocal	1186000.0000
Solution quality estimate total_estimate	0.7835
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	14.5 Å
Skewness Skewness skewness	0.211
Kurtosis Kurtosis kurtosis	-0.413
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	200700.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.910; Stabil: 1.000; Sysdev: 0.499; Positv: 1.000; Valcen: 0.995; Smooth: 0.959

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1dfna1
Class class	g — Small proteins
Fold Fold fold	g.9 — Defensin-like
Superfamily Superfamily superfamily	g.9.1 — Defensin-like
Family Family family	g.9.1.1 — Defensin

Domain ID domain_id	d1dfna2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d1dfnb1
Class class	g — Small proteins
Fold Fold fold	g.9 — Defensin-like
Superfamily Superfamily superfamily	g.9.1 — Defensin-like
Family Family family	g.9.1.1 — Defensin

Domain ID domain_id	d1dfnb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

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8. Citations (3)

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Unit-cell length a length_a	30.800 Å
Unit-cell length b length_b	45.000 Å
Unit-cell length c length_c	40.300 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	8

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1900
R_work r_work	—
R_free r_free	—

Description description	DEFENSIN HNP-3
Molecular weight formula_weight	3496.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	514

CRYSTAL STRUCTURE OF DEFENSIN HNP-3, AN AMPHIPHILIC DIMER: MECHANISMS OF MEMBRANE PERMEABILIZATION

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

DEFENSIN HNP-3

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

8. Citations (3)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	44

fit	/app/data/saxs_computation/df/1dfn/1dfn.fit
pddf	/app/data/pr_computation/df/1dfn/1dfn.pr.out
profile	/app/data/saxs_computation/df/1dfn/1dfn.dat