3vhm

Crystal structure of NPC-biotin-avidin complex

Method: X-RAY DIFFRACTION D_max: 67.0 Å Quality: REASONABLE

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

Avidin

OrganismNot specified

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 25–147 Chain B； UniProt 25–147 Chain C； UniProt 25–147 Chain D； UniProt 25–147	Fragment：UNP residues 25-147	NPK 5-[(3aS,4R,6aR)-1-{[(1R)-1-(6-nitro-1,3-benzodioxol-5-yl)ethoxy]carbonyl}-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoic acid × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；2.5-2.7M ammonium sulfate, 0.1M sodium citrate(pH 4.0-5.0), vapor diffusion, sitting drop, temperature 293K	Resolution 2.00 Å R-free 0.230

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 3VHM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AVD THREE-DIMENSIONAL STRUCTURE OF THE TETRAGONAL CRYSTAL FORM OF EGG-WHITE AVIDIN IN ITS FUNCTIONAL COMPLEX WITH BIOTIN AT 2.7 ANGSTROMS RESOLUTION Deposited 1993-03-05	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 25–152（128 aa） Chain B 25–152（128 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 BTN BIOTIN × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.70 Å
1AVE CRYSTAL STRUCTURE OF HEN EGG-WHITE APO-AVIDIN IN RELATION TO ITS THERMAL STABILITY PROPERTIES Deposited 1993-03-05	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 25–152（128 aa） Chain B 25–152（128 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å
1IJ8 CRYSTAL STRUCTURE OF LITE AVIDIN-BNI COMPLEX Deposited 2001-04-25	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 25–152（128 aa） Chain B 25–152（128 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 BNI 5-(2-OXO-HEXAHYDRO-THIENO[3,4-D]IMIDAZOL-6-YL)-PENTANOIC ACID (4-NITRO-PHENYL)-AMIDE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；293 K；12% PEG2000, 0.1M imidazole malate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.234
1LDO avidin-norbioitn complex Deposited 2002-04-09	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 25–152（128 aa） Chain B 25–152（128 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 SNR NORBIOTIN × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；293 K；12% PEG 1000, 0.1 immidazole malate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.20 Å R-free 0.241
1LDQ avidin-homobiotin complex Deposited 2002-04-09	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 25–152（128 aa） Chain B 25–152（128 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 SHM HOMOBIOTIN × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；293 K；12% PEG 1000, 0,1M immidazole malate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.70 Å R-free 0.276
1LEL The avidin BCAP complex Deposited 2002-04-10	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 25–152（128 aa） Chain B 25–152（128 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 BH7 E-AMINO BIOTINYL CAPROIC ACID × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；293 K；12% PEG 1000, 0.1M immidazole malate, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.90 Å R-free 0.284
1NQN Structure of Avm-W110K (W110K mutant of avidin) Deposited 2003-01-22	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 26–147（122 aa） Chain B 26–147（122 aa）	Mutation：W110K Mutation：W110K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；32% MPEG 2k, 0.1M Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 20K	Resolution 1.80 Å R-free 0.227
1RAV RECOMBINANT AVIDIN Deposited 1998-03-27	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 26–152（127 aa） Chain B 26–152（127 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.2；RECOMBINANT AVIDIN WAS CRYSTALLIZED FROM 9% W/V PEG 8000. PH 7.2 0.05 M TRIS BUFFER AT 22 C BY VAPOUR DIFFUSION TECHNIQUES., vapor diffusion	Resolution 2.20 Å
1VYO Crystal structure of avidin Deposited 2004-05-03	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 25–152（128 aa） Chain B 25–152（128 aa）	Not recorded	GOL GLYCEROL × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；295 K；Equal volumes (1 ul) of protein (0.5 mg/ml) in 50 mM Na acetate (pH 4) + 20 mM NaCl and well solution of 0.1 M MES (pH 6.6) + 24% PEG 8000 + 0.2 M Mg acetate	Resolution 1.48 Å R-free 0.190
2A5B Avidin complexed with 8-oxodeoxyguanosine Deposited 2005-06-30	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 25–148（124 aa） Chain B 25–148（124 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 8HG 2'-DEOXY-8-OXOGUANOSINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；290 K；PEG 8000, Sodium Citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 290.0K	Resolution 2.49 Å R-free 0.310
2A5C Structure of Avidin in complex with the ligand 8-oxodeoxyadenosine Deposited 2005-06-30	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 25–147（123 aa） Chain B 25–147（123 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 8DA 8-OXODEOXYADENOSINE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；290 K；0.2M ammonium sulphate, 0.1M Na Cacodylate pH6.5, 30% w/v PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 2.50 Å R-free 0.308
2A8G Structure of Avidin in complex with the ligand deoxyguanosine Deposited 2005-07-08	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 27–152（126 aa） Chain B 27–152（126 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 GNG 2'-DEOXY-GUANOSINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；291 K；50mM Na Citrate, 20% PEG 8000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.99 Å R-free 0.268
2AVI THREE-DIMENSIONAL STRUCTURES OF AVIDIN AND THE AVIDIN-BIOTIN COMPLEX Deposited 1993-04-23	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 25–152（128 aa） Chain B 25–152（128 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 BTN BIOTIN × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.00 Å
2C4I Crystal structure of engineered avidin Deposited 2005-10-19	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 27–80（54 aa） Chain A 99–147（49 aa）	Not recorded	BTN BIOTIN × 4 SO4 SULFATE ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.95 Å R-free 0.246
2CAM AVIDIN MUTANT (K3E,K9E,R26D,R124L) Deposited 1998-03-27	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 26–152（127 aa） Chain B 26–152（127 aa）	Mutation：K3E, K9E, R26D, R124L Mutation：K3E, K9E, R26D, R124L	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.7；295 K；RECOMBINANT AVIDIN WAS CRYSTALLIZED FROM AMMONIUM SULFATE 2M. PH 5.7 0.05 M PHOSPHATE BUFFER AT 22 C BY VAPOUR DIFFUSION TECHNIQUES., vapor diffusion, temperature 295K	Resolution 2.20 Å
2MF6 Solution NMR structure of Chimeric Avidin, ChiAVD(I117Y), in the biotin bound form Deposited 2013-10-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 25–61（37 aa） Fragment：P02701 Residues 25-61, 85-152 and P56734 residues 62-82 Chain A 85–152（68 aa） Fragment：P02701 Residues 25-61, 85-152 and P56734 residues 62-82 Chain B 25–61（37 aa） Fragment：P02701 Residues 25-61, 85-152 and P56734 residues 62-82 Chain B 85–152（68 aa） Fragment：P02701 Residues 25-61, 85-152 and P56734 residues 62-82 Chain C 25–61（37 aa） Fragment：P02701 Residues 25-61, 85-152 and P56734 residues 62-82 Chain C 85–152（68 aa） Fragment：P02701 Residues 25-61, 85-152 and P56734 residues 62-82 Chain D 25–61（37 aa） Fragment：P02701 Residues 25-61, 85-152 and P56734 residues 62-82 Chain D 85–152（68 aa） Fragment：P02701 Residues 25-61, 85-152 and P56734 residues 62-82	Mutation：I117Y Mutation：I117Y Mutation：I117Y Mutation：I117Y Mutation：I117Y Mutation：I117Y Mutation：I117Y Mutation：I117Y	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；333 K；Pressure 1 NMR measurement conditions pH 6.5；333 K；Pressure 1 NMR sample composition 0.7-1.2 mM [U-13C; U-15N] avidin-1, 0.7-1.2 mM d-biotin-2, 93 % H2O-3, 7 % D2O-4, 93% H2O/7% D2O \| 93% H2O/7% D2O NMR sample composition 0.7-1.2 mM [U-13C; U-15N] avidin-5, 0.7-1.2 mM d-biotin-6, 100 % D2O-7, 100% D2O \| 100% D2O	Resolution not provided
3FDC Crystal Structure of Avidin Deposited 2008-11-25	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 25–152（128 aa） Chain B 25–152（128 aa）	Not recorded	BTF iron(II) tetracyano-5-(2-Oxo-hexahydro-thieno[3,4-d]imidazol-6-yl)-pentanoic acid (4'-methyl-[2,2']bipyridinyl-4-ylmethyl)-amide × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；296 K；25% PEG 3000, 100 mM sodium acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 296.0K	Resolution 3.10 Å R-free 0.330
3MM0 Crystal structure of chimeric avidin Deposited 2010-04-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 25–61（37 aa） Fragment：P02701 Residues 25-61, 85-152 and P56734 residues 62-82 Chain A 85–152（68 aa） Fragment：P02701 Residues 25-61, 85-152 and P56734 residues 62-82 Chain B 25–61（37 aa） Fragment：P02701 Residues 25-61, 85-152 and P56734 residues 62-82 Chain B 85–152（68 aa） Fragment：P02701 Residues 25-61, 85-152 and P56734 residues 62-82 Chain C 25–61（37 aa） Fragment：P02701 Residues 25-61, 85-152 and P56734 residues 62-82 Chain C 85–152（68 aa） Fragment：P02701 Residues 25-61, 85-152 and P56734 residues 62-82 Chain D 25–61（37 aa） Fragment：P02701 Residues 25-61, 85-152 and P56734 residues 62-82 Chain D 85–152（68 aa） Fragment：P02701 Residues 25-61, 85-152 and P56734 residues 62-82	Mutation：I141Y Mutation：I141Y Mutation：I141Y Mutation：I141Y Mutation：I141Y Mutation：I141Y Mutation：I141Y Mutation：I141Y	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；pH 8.3；293 K；20% Polyethylene glycol monomethyl ether 5000, 0.1M Tris (pH 8.3), and 9mM ammonium sulfate, microbatch, temperature 293K	Resolution 2.70 Å R-free 0.309
3MM0 Crystal structure of chimeric avidin Deposited 2010-04-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain E 25–61（37 aa） Fragment：P02701 Residues 25-61, 85-152 and P56734 residues 62-82 Chain E 85–152（68 aa） Fragment：P02701 Residues 25-61, 85-152 and P56734 residues 62-82 Chain F 25–61（37 aa） Fragment：P02701 Residues 25-61, 85-152 and P56734 residues 62-82 Chain F 85–152（68 aa） Fragment：P02701 Residues 25-61, 85-152 and P56734 residues 62-82 Chain G 25–61（37 aa） Fragment：P02701 Residues 25-61, 85-152 and P56734 residues 62-82 Chain G 85–152（68 aa） Fragment：P02701 Residues 25-61, 85-152 and P56734 residues 62-82 Chain H 25–61（37 aa） Fragment：P02701 Residues 25-61, 85-152 and P56734 residues 62-82 Chain H 85–152（68 aa） Fragment：P02701 Residues 25-61, 85-152 and P56734 residues 62-82	Mutation：I141Y Mutation：I141Y Mutation：I141Y Mutation：I141Y Mutation：I141Y Mutation：I141Y Mutation：I141Y Mutation：I141Y	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；pH 8.3；293 K；20% Polyethylene glycol monomethyl ether 5000, 0.1M Tris (pH 8.3), and 9mM ammonium sulfate, microbatch, temperature 293K	Resolution 2.70 Å R-free 0.309
3MM0 Crystal structure of chimeric avidin Deposited 2010-04-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain I 25–61（37 aa） Fragment：P02701 Residues 25-61, 85-152 and P56734 residues 62-82 Chain I 85–152（68 aa） Fragment：P02701 Residues 25-61, 85-152 and P56734 residues 62-82 Chain K 25–61（37 aa） Fragment：P02701 Residues 25-61, 85-152 and P56734 residues 62-82 Chain K 85–152（68 aa） Fragment：P02701 Residues 25-61, 85-152 and P56734 residues 62-82	Mutation：I141Y Mutation：I141Y Mutation：I141Y Mutation：I141Y	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；pH 8.3；293 K；20% Polyethylene glycol monomethyl ether 5000, 0.1M Tris (pH 8.3), and 9mM ammonium sulfate, microbatch, temperature 293K	Resolution 2.70 Å R-free 0.309
3MM0 Crystal structure of chimeric avidin Deposited 2010-04-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Insufficient information Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain M 25–61（37 aa） Fragment：P02701 Residues 25-61, 85-152 and P56734 residues 62-82 Chain M 85–152（68 aa） Fragment：P02701 Residues 25-61, 85-152 and P56734 residues 62-82 Chain N 25–61（37 aa） Fragment：P02701 Residues 25-61, 85-152 and P56734 residues 62-82 Chain N 85–152（68 aa） Fragment：P02701 Residues 25-61, 85-152 and P56734 residues 62-82	Mutation：I141Y Mutation：I141Y Mutation：I141Y Mutation：I141Y	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions MICROBATCH；pH 8.3；293 K；20% Polyethylene glycol monomethyl ether 5000, 0.1M Tris (pH 8.3), and 9mM ammonium sulfate, microbatch, temperature 293K	Resolution 2.70 Å R-free 0.309
3VGW Crystal structure of monoAc-biotin-avidin complex Deposited 2011-08-21	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 25–147（123 aa） Fragment：UNP residues 25-147 Chain B 25–147（123 aa） Fragment：UNP residues 25-147 Chain C 25–147（123 aa） Fragment：UNP residues 25-147 Chain D 25–147（123 aa） Fragment：UNP residues 25-147	Not recorded	NVZ 5-[(3aS,4S,6aR)-1-acetyl-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoic acid × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；2.5-2.7M ammonium sulfate, 0.1M sodium citrate(pH 4.0-5.0), VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.60 Å R-free 0.215
3VGW Crystal structure of monoAc-biotin-avidin complex Deposited 2011-08-21	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain E 25–147（123 aa） Fragment：UNP residues 25-147 Chain F 25–147（123 aa） Fragment：UNP residues 25-147 Chain G 25–147（123 aa） Fragment：UNP residues 25-147 Chain H 25–147（123 aa） Fragment：UNP residues 25-147	Not recorded	NVZ 5-[(3aS,4S,6aR)-1-acetyl-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoic acid × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；2.5-2.7M ammonium sulfate, 0.1M sodium citrate(pH 4.0-5.0), VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.60 Å R-free 0.215
3VHH Crystal structure of DiMe-biotin-avidin complex Deposited 2011-08-25	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 25–147（123 aa） Fragment：UNP residues 25-147 Chain B 25–147（123 aa） Fragment：UNP residues 25-147 Chain C 25–147（123 aa） Fragment：UNP residues 25-147 Chain D 25–147（123 aa） Fragment：UNP residues 25-147	Not recorded	VHH 5-[(3aS,4S,6aR)-1,3-dimethyl-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoic acid × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；2.5-2.7M ammonium sulfate, 0.1M sodium citrate(pH 4.0-5.0), vapor diffusion, sitting drop, temperature 293K	Resolution 2.26 Å R-free 0.260
3VHI Crystal structure of monoZ-biotin-avidin complex Deposited 2011-08-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 26–147（122 aa） Fragment：UNP residues 26-147 Chain B 26–147（122 aa） Fragment：UNP residues 26-147 Chain C 26–147（122 aa） Fragment：UNP residues 26-147 Chain D 26–147（122 aa） Fragment：UNP residues 26-147	Not recorded	VHI 5-{(3aS,4S,6aR)-1-[(benzyloxy)carbonyl]-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl}pentanoic acid × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；293 K；2.5-2.7M ammonium sulfate, 0.1M sodium citrate (pH 4.0-5.0), vapor diffusion, sitting drop, temperature 293K	Resolution 1.76 Å R-free 0.226
4I60 Crystal structure of avidin - biotinylruthenocene complex Deposited 2012-11-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 25–152（128 aa）	Not recorded	B1R [(1,2,3,4,5-eta)-cyclopentadienyl][(1,2,3,4,5-eta)-{5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoyl}cyclopentadienyl]ruthenium × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；35% pentaerythritol propoxylate, 0.05M HEPES, 0.2M KCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.50 Å R-free 0.211
4JHQ Crystal structure of avidin - 6-(6-biotinamidohexanamido)hexanoylferrocene complex Deposited 2013-03-05	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 25–152（128 aa） Chain B 25–152（128 aa）	Not recorded	B6F [(1,2,3,4,5-eta)-cyclopentadienyl][(1,2,3,4,5-eta)-{6-[(6-{[5-(2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl)pentanoyl]amino}hexanoyl)amino]hexanoyl}cyclopentadienyl]iron × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；28% mme PEG 5K, 0.2M magnesium formate, 0.1M Bis-Tris, pH 6.5, VAPOR DIFFUSION, temperature 293K	Resolution 1.99 Å R-free 0.210
4U46 Crystal structure of an avidin mutant Deposited 2014-07-23	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 23–152（130 aa） Fragment：UNP residues 25-152 Chain B 23–152（130 aa） Fragment：UNP residues 25-152	Not recorded	CL CHLORIDE ION × 24	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；Well solution: 0.2 M sodium chloride, 0.1 M sodium cacodylate, 2.0 M ammonium sulphate	Resolution 1.95 Å R-free 0.214
5CHK Crystal structure of avidin - HABA complex (hexagonal crystal form) Deposited 2015-07-10	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 25–152（128 aa） Fragment：UNP residues 25-152	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 55R 2-[2-(4-oxocyclohexa-2,5-dien-1-ylidene)hydrazinyl]benzoic acid × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；292.15 K；0.1M sodium citrate tribasic dehydrate pH 4.5, 24% w/v polyethylene glycol 1000	Resolution 2.20 Å R-free 0.227
5HLM Crystal structure of avidin complex with a ferrocene biotin derivative Deposited 2016-01-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 25–152（128 aa） Chain B 25–152（128 aa） Chain C 25–152（128 aa） Chain D 25–152（128 aa）	Not recorded	B9F [(1,2,3,4,5-eta)-cyclopentadienyl]{(1,2,3,4,5-eta)-1-[1-hydroxy-5-(2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl)pentyl]cyclopentadienyl}iron × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292.15 K；0.2M potassium thiocyanate, 0.1M BIS-TRIS pH 6.5 and 22% w/v polyethylene glycol 3350	Resolution 2.50 Å R-free 0.254
5IRU Crystal structure of avidin in complex with 1-biotinylpyrene Deposited 2016-03-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 25–152（128 aa） Chain B 25–152（128 aa） Chain C 25–152（128 aa） Chain D 25–152（128 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 B9P 1-biotinylpyrene × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；292.15 K；28% w/v polyethylene glycol monomethyl ether 2000, 0.1 M Bis-Tris, 0.1 M trimethylamine hydrochloride	Resolution 2.00 Å R-free 0.265
5IRW Crystal structure of avidin in complex with 1-desthiobiotinylpyrene Deposited 2016-03-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 25–152（128 aa） Chain B 25–152（128 aa） Chain C 25–152（128 aa） Chain D 25–152（128 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 D9P 1-desthiobiotinylpyrene × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；292.15 K；Morpheus Screen (Molecular Dimensions) A1 solution (0.1 M IMIDAZOLE/MES MONOHYDRATE (ACID) BUFFER PH 6.5, 10% W/V POLYETHYLENE GLYCOL 20000, 20% V/V PEG 500 MME, 0.03 M MAGNESIUM CHLORIDE HEXAHYDRATE AND 0.03 M CALCIUM CHLORIDE DIHYDRATE), VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 292.15K	Resolution 2.10 Å R-free 0.231
5LUR An avidin mutant Deposited 2016-09-09	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 21–152（132 aa） Chain B 21–152（132 aa）	Not recorded	STR PROGESTERONE × 4 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；Drop size: 150 nl of protein-ligand solution and well solution. Protein-ligand solution: 1.8 mg/ml of protein solution (20 mM sodium phosphate, 1M sodium chloride, 20mM imidazole, pH 7.4) and 50 mM ligand solution (1.57 mg in 100 microL of water) were mixed in 10:1 (v/v) ratio. Well solution: 0.18 M sodium chloride, 0.09 M sodium cacodylate (pH 6.5) and 1.8 M ammonium sulfate.	Resolution 2.70 Å R-free 0.240
5MYQ Crystal structure of avidin in complex with ferrocene homobiotin derivative Deposited 2017-01-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 25–152（128 aa） Chain B 25–152（128 aa） Chain C 25–152（128 aa） Chain D 25–152（128 aa）	Not recorded	HBF ferrocene homobiotin derivative × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 IOD IODIDE ION × 21	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292.15 K；0.2 M ammonium iodide, 22 % w/v PEG 3350	Resolution 1.89 Å R-free 0.232
6XND Avidin-Biotin-Phenol Deposited 2020-07-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 25–152（128 aa） Chain B 25–152（128 aa） Chain C 25–152（128 aa） Chain D 25–152（128 aa）	Not recorded	V8M N-[2-(2-hydroxy-5-nitrophenyl)ethyl]-5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanamide × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；300 K；0.1 M Tris, pH 7.0, and 25% (w/v) PEG 1500	Resolution 1.58 Å R-free 0.236
7P4Z Crystal structure of avidin from hen egg white in space group C2 Deposited 2021-07-13	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 27–147（121 aa） Chain B 27–147（121 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；10% w/v PEG 8000, 20% v/v ethylene glycol, 0.1 M MES/Imidazole pH 6.5, 0.4% of each Anaesthetic alkaloid (Morpheus Fusion screen, well H12)	Resolution 2.20 Å R-free 0.291
7ZN1 Avidin + Biotin-Tempo Deposited 2022-04-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–152（152 aa） Chain B 1–152（152 aa） Chain C 1–152（152 aa） Chain D 1–152（152 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 KFL 6-[(3~{a}~{S},4~{S},6~{a}~{R})-2-oxidanylidene-1,3,3~{a},4,6,6~{a}-hexahydrothieno[3,4-d]imidazol-4-yl]-~{N}-(2,2,6,6-tetramethyl-1-oxidanyl-piperidin-4-yl)hexanamide × 4 ZN ZINC ION × 4 NA SODIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298.15 K；0.2 M Zinc Acetate dihydrate 22% w/v PEG3350	Resolution 2.33 Å R-free 0.279
7ZYL Avidin + Biotin-Tempo Deposited 2022-05-25	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–152（152 aa） Chain B 1–152（152 aa） Chain C 1–152（152 aa） Chain D 1–152（152 aa）	Not recorded	KFL 6-[(3~{a}~{S},4~{S},6~{a}~{R})-2-oxidanylidene-1,3,3~{a},4,6,6~{a}-hexahydrothieno[3,4-d]imidazol-4-yl]-~{N}-(2,2,6,6-tetramethyl-1-oxidanyl-piperidin-4-yl)hexanamide × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.08 Å
8CK7 Avidin complexed to theophylline Deposited 2023-02-14	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 25–148（124 aa） Chain B 25–148（124 aa）	Not recorded	GOL GLYCEROL × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 TEP THEOPHYLLINE × 4 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M Bis-Tris-Propane pH 8.5, 1.7-2.3 M w/v Ammonium Sulfate, 1-5% v/v MPD	Resolution 2.20 Å R-free 0.233

35 other PDB entries and 39 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	AVID_CHICK
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–123； UniProt 25–147 Author chain B； PDBConstruct 1–123； UniProt 25–147 Author chain C； PDBConstruct 1–123； UniProt 25–147 Author chain D； PDBConstruct 1–123； UniProt 25–147

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	3vhm
Deposition date deposition_date	2011-08-29
Structure title title	Crystal structure of NPC-biotin-avidin complex
Keywords keywords	beta barrel, BIOTIN-BINDING PROTEIN; BIOTIN-BINDING PROTEIN
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	23.13 Å
Radius of gyration Rg (electron density) rg_electron	21.85 Å
Forward intensity I(0) i0	58766000.00
Molecular weight molecular_weight	57641.0 kDa
Excluded volume excluded_volume	71212 Å³
Envelope volume envelope_volume	81659 Å³
Hydration-shell volume shell_volume	29539 Å³
Envelope diameter envelope_diameter	67.4 Å
Shell Rg shell_rg	29.87 Å
Envelope Rg envelope_rg	22.17 Å
Shape Rg shape_rg	21.79 Å
Total Rg total_rg	22.87 Å
Total atoms total_atoms	4039
Residues n_residues	488
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	67.0 Å
Rg (real space) rg_real	22.94 Å
Rg uncertainty (real space) rg_real_error	0.29 Å
I(0) (real space) i0_real	5.8770e+07
I(0) uncertainty (real space) i0_real_error	7.0400e+05
Rg (reciprocal space) rg_reciprocal	22.98 Å
I(0) (reciprocal space) i0_reciprocal	58770000.0000
Solution quality estimate total_estimate	0.7498
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	30.9 Å
Skewness Skewness skewness	0.041
Kurtosis Kurtosis kurtosis	-0.571
Angular range angular_range	— – 0.3450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	18230000.0000
Real-space data points n_real_points	66
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.964; Stabil: 1.000; Sysdev: 0.307; Positv: 1.000; Valcen: 0.976; Smooth: 0.956

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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	Avidin
Molecular weight formula_weight	13716.4 kDa
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	4241

ARKCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYITAVTATSNEIKESPLHGTQNTINKRTQPTFGFTVNWKFSESTTVFTGQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRL

Entity 2 Entity 2 non-polymer

Description description	;5-[(3aS,4R,6aR)-1-{[(1R)-1-(6-nitro-1,3-benzodioxol-5-yl)ethoxy]carbonyl}-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoic acid ;
Molecular weight formula_weight	481.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	202

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3vhma_
Class class	b — All beta proteins
Fold Fold fold	b.61 — Streptavidin-like
Superfamily Superfamily superfamily	b.61.1 — Avidin/streptavidin
Family Family family	b.61.1.1 — Avidin/streptavidin

Domain ID domain_id	d3vhmb_
Class class	b — All beta proteins
Fold Fold fold	b.61 — Streptavidin-like
Superfamily Superfamily superfamily	b.61.1 — Avidin/streptavidin
Family Family family	b.61.1.1 — Avidin/streptavidin

Domain ID domain_id	d3vhmc_
Class class	b — All beta proteins
Fold Fold fold	b.61 — Streptavidin-like
Superfamily Superfamily superfamily	b.61.1 — Avidin/streptavidin
Family Family family	b.61.1.1 — Avidin/streptavidin

Domain ID domain_id	d3vhmd_
Class class	b — All beta proteins
Fold Fold fold	b.61 — Streptavidin-like
Superfamily Superfamily superfamily	b.61.1 — Avidin/streptavidin
Family Family family	b.61.1.1 — Avidin/streptavidin

CATH v4.4 (4 domains)

Domain ID domain_id	3vhmA00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	30 — Avidin-like

Domain ID domain_id	3vhmB00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	30 — Avidin-like

Domain ID domain_id	3vhmC00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	30 — Avidin-like

Domain ID domain_id	3vhmD00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	128 — Lipocalin
Homologous superfamily homologous superfamily	30 — Avidin-like

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8. Citations (1)

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Unit-cell length a length_a	131.020 Å
Unit-cell length b length_b	73.535 Å
Unit-cell length c length_c	81.180 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	120.02 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	37.520 Å
R factor r_factor	0.1907
R_work r_work	0.1885
R_free r_free	0.2303

fit	/app/data/saxs_computation/vh/3vhm/3vhm.fit
pddf	/app/data/pr_computation/vh/3vhm/3vhm.pr.out
profile	/app/data/saxs_computation/vh/3vhm/3vhm.dat