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2avi

THREE-DIMENSIONAL STRUCTURES OF AVIDIN AND THE AVIDIN-BIOTIN COMPLEX

Method: X-RAY DIFFRACTION Dmax: 65.8 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

AVIDIN

Gallus gallus

UniProt P02701

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 25–152 Chain B； UniProt 25–152 Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 BTN BIOTIN × 4 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 3.00 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 2AVI 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 ligand/ion 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 ligand/ion 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 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 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 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 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 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 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 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 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 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
2C4I Crystal structure of engineered avidin Deposited 2005-10-19 Different construct Different oligomeric state Different ligand/ion 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 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 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） 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 construct Different mutation/modification 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 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） 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 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） 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
3VHM Crystal structure of NPC-biotin-avidin complex Deposited 2011-08-29 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） 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 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
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 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 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 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）
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 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）
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 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）
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 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 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）
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 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）
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 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 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 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 mutation/modification 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 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 1–128； UniProt 25–152 Author chain B； PDBConstruct 1–128； UniProt 25–152

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

SAXS profile for 2avi

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2avi
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2avi
Deposition date deposition_date1993-04-23
Structure title titleTHREE-DIMENSIONAL STRUCTURES OF AVIDIN AND THE AVIDIN-BIOTIN COMPLEX
Keywords keywordsBIOTIN BINDING PROTEIN; BIOTIN BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier21.42 Å
Radius of gyration Rg (electron density) rg_electron20.23 Å
Forward intensity I(0) i014256800.00
Molecular weight molecular_weight27793.0 kDa
Excluded volume excluded_volume34542 ų
Envelope volume envelope_volume43532 ų
Hydration-shell volume shell_volume18213 ų
Envelope diameter envelope_diameter66.2 Å
Shell Rg shell_rg26.04 Å
Envelope Rg envelope_rg20.08 Å
Shape Rg shape_rg20.21 Å
Total Rg total_rg21.10 Å
Total atoms total_atoms1952
Residues n_residues242
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax65.8 Å
Rg (real space) rg_real21.27 Å
Rg uncertainty (real space) rg_real_error0.42 Å
I(0) (real space) i0_real1.4260e+07
I(0) uncertainty (real space) i0_real_error1.6930e+05
Rg (reciprocal space) rg_reciprocal21.30 Å
I(0) (reciprocal space) i0_reciprocal14260000.0000
Solution quality estimate total_estimate0.9056
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary31.0 Å
Skewness Skewness skewness0.016
Kurtosis Kurtosis kurtosis-0.608
Angular range angular_range— – 0.3700 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1855000.0000
Real-space data points n_real_points69
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.933; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.969
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2avia_
Class classb — All beta proteins
Fold Fold foldb.61 — Streptavidin-like
Superfamily Superfamily superfamilyb.61.1 — Avidin/streptavidin
Family Family familyb.61.1.1 — Avidin/streptavidin
Domain ID domain_idd2avib_
Class classb — All beta proteins
Fold Fold foldb.61 — Streptavidin-like
Superfamily Superfamily superfamilyb.61.1 — Avidin/streptavidin
Family Family familyb.61.1.1 — Avidin/streptavidin

CATH v4.4 (2 domains)

Domain ID domain_id2aviA00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology128 — Lipocalin
Homologous superfamily homologous superfamily30 — Avidin-like
Domain ID domain_id2aviB00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology128 — Lipocalin
Homologous superfamily homologous superfamily30 — Avidin-like
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8. Citations (1)

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9. Files and Curves (10)