5vig

Crystal structure of anti-Zika antibody Z006 bound to Zika virus envelope protein DIII

Method: X-RAY DIFFRACTION D_max: 114.5 Å Quality: EXCELLENT

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

Fab heavy chain

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain H； UniProt 129–242	Not recorded	Fab light chain × 1 （P0DOX7） Zika virus envelope protein DIII × 1 （A0A1I9ZK43）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5；295 K；10% isopropanol, 0.1M sodium citrate tribasic dihydrate pH 5.0, 26% PEG 400	Resolution 3.00 Å R-free 0.257
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 129–242	Not recorded	Fab light chain × 1 （P0DOX7） Zika virus envelope protein DIII × 1 （A0A1I9ZK43） FLC CITRATE ANION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5；295 K；10% isopropanol, 0.1M sodium citrate tribasic dihydrate pH 5.0, 26% PEG 400	Resolution 3.00 Å R-free 0.257

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 5VIG	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3MNW Crystal structure of the non-neutralizing HIV antibody 13H11 Fab fragment with a gp41 MPER-derived peptide in a helical conformation Deposited 2010-04-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 133–241（109 aa） Fragment：mouse Fv,human Fc	Not recorded	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.2；298 K；Reservoir: Qiagen Classics II screen H10 (0.2 M K Na tartrate, 20% PEG 3350). Drop: 0.6 uL protein + 0.4 uL reservoir., pH 7.2, VAPOR DIFFUSION, temperature 298K	Resolution 2.20 Å R-free 0.253
3MNW Crystal structure of the non-neutralizing HIV antibody 13H11 Fab fragment with a gp41 MPER-derived peptide in a helical conformation Deposited 2010-04-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 133–241（109 aa） Fragment：mouse Fv,human Fc	Not recorded	EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.2；298 K；Reservoir: Qiagen Classics II screen H10 (0.2 M K Na tartrate, 20% PEG 3350). Drop: 0.6 uL protein + 0.4 uL reservoir., pH 7.2, VAPOR DIFFUSION, temperature 298K	Resolution 2.20 Å R-free 0.253
3MNZ Crystal structure of the non-neutralizing HIV antibody 13H11 Fab fragment with a gp41 MPER-derived peptide bearing Ala substitutions in a helical conformation Deposited 2010-04-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 133–241（109 aa） Fragment：mouse Fv,human Fc	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.2；298 K；Reservoir: Qiagen Classics II, condition with 0.2 M K Na tartrate, 20% PEG 3350. Drop: 0.6 uL protein + 0.4 uL reservoir, pH 7.2, VAPOR DIFFUSION, temperature 298K	Resolution 1.80 Å R-free 0.215
4EOW Crystal structure of a disease-associated anti-human GM-CSF autoantibody MB007 Deposited 2012-04-16	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 137–237（101 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.4；277 K；19% PEG 4000, 0.1M ammonium sulphate, 0.1M sodium acetate, pH 3.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.97 Å R-free 0.257
4YDV STRUCTURE OF THE ANTIBODY 7B2 THAT CAPTURES HIV-1 VIRIONS Deposited 2015-02-23	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 132–241（110 aa） Fragment：HIV ANTIBODY 7B2 HEAVY CHAIN,HIV ANTIBODY 7B2 HEAVY CHAIN	Mutation：YES,YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 3.5；298 K；6% PEG 20,000, 5% 2-PROPANOL, 0.1 M CITRIC ACID PH 3.5	Resolution 2.70 Å R-free 0.223
4YDV STRUCTURE OF THE ANTIBODY 7B2 THAT CAPTURES HIV-1 VIRIONS Deposited 2015-02-23	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 132–241（110 aa） Fragment：HIV ANTIBODY 7B2 HEAVY CHAIN,HIV ANTIBODY 7B2 HEAVY CHAIN	Mutation：YES,YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 3.5；298 K；6% PEG 20,000, 5% 2-PROPANOL, 0.1 M CITRIC ACID PH 3.5	Resolution 2.70 Å R-free 0.223
5C7K Crystal structure BG505 SOSIP gp140 HIV-1 Env trimer bound to broadly neutralizing antibodies PGT128 and 8ANC195 Deposited 2015-06-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: octadecameric	Chain A 129–240（112 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；280 K；0.05 M lithium sulfate, 0.05 M sodium sulfate, 26% (w/v) PEG 400 and 0.1 M Tris-HCl pH 8.3	Resolution 4.60 Å R-free 0.295
5CUS Crystal Structure of sErbB3-Fab3379 Complex Deposited 2015-07-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 20–239（220 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；PEG 3350, Ammonium Citrate, Sodium Thiocyanate	Resolution 3.20 Å R-free 0.278
5CUS Crystal Structure of sErbB3-Fab3379 Complex Deposited 2015-07-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 20–239（220 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；PEG 3350, Ammonium Citrate, Sodium Thiocyanate	Resolution 3.20 Å R-free 0.278
5CUS Crystal Structure of sErbB3-Fab3379 Complex Deposited 2015-07-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain J 20–239（220 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；PEG 3350, Ammonium Citrate, Sodium Thiocyanate	Resolution 3.20 Å R-free 0.278
5CUS Crystal Structure of sErbB3-Fab3379 Complex Deposited 2015-07-25	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain K 20–239（220 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；PEG 3350, Ammonium Citrate, Sodium Thiocyanate	Resolution 3.20 Å R-free 0.278
5D9Q Crystal Structure of the BG505 SOSIP gp140 HIV-1 Env trimer in Complex with the Broadly Neutralizing Fab PGT122 and scFv NIH45-46 Deposited 2015-08-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: pentadecameric	Chain F 132–239（108 aa） Chain H 132–239（108 aa） Chain N 132–239（108 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 18	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2.4 M ammonium sulfate, 0.1 M Tris, pH 8.0	Resolution 4.40 Å R-free 0.320
5VEB Crystal structure of a Fab binding to extracellular domain 5 of Cadherin-6 Deposited 2017-04-04	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 126–243（118 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	A2G 2-acetamido-2-deoxy-alpha-D-galactopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；20% (w/v) PEG3350, 0.2M di-ammonium hydrogen citrate	Resolution 2.34 Å R-free 0.252
5VEB Crystal structure of a Fab binding to extracellular domain 5 of Cadherin-6 Deposited 2017-04-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 126–243（118 aa）	Not recorded	A2G 2-acetamido-2-deoxy-alpha-D-galactopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；294 K；20% (w/v) PEG3350, 0.2M di-ammonium hydrogen citrate	Resolution 2.34 Å R-free 0.252
5VIC Crystal structure of anti-Zika antibody Z004 bound to DENV-1 Envelope protein DIII Deposited 2017-04-14	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 126–242（117 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；295 K；0.1M sodium acetate trihydrate pH 4.5, 30% w/v PEG 1500	Resolution 3.00 Å R-free 0.286
5VIY BG505 SOSIP.664 in complex with broadly neutralizing antibodies BG1 and 8ANC195 Deposited 2017-04-17	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 Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain H 137–236（100 aa） Chain J 137–236（100 aa） Chain K 137–237（101 aa） Chain M 137–237（101 aa） Chain O 137–237（101 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 13	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 6.20 Å
5VJ6 BG505 SOSIP.664 in complex with broadly neutralizing antibodies PG9 and 8ANC195 Deposited 2017-04-18	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain M 137–237（101 aa） Chain O 137–237（101 aa） Chain Q 137–237（101 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE	Resolution 11.50 Å
5VL3 CD22 d1-d3 in complex with therapeutic Fab Epratuzumab Deposited 2017-04-24	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 132–239（108 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；20 mM Tris pH 8.0 and 150 mM NaCl, 5mg/mL	Resolution 3.10 Å R-free 0.295
5VL3 CD22 d1-d3 in complex with therapeutic Fab Epratuzumab Deposited 2017-04-24	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 132–239（108 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；20 mM Tris pH 8.0 and 150 mM NaCl, 5mg/mL	Resolution 3.10 Å R-free 0.295
5VL3 CD22 d1-d3 in complex with therapeutic Fab Epratuzumab Deposited 2017-04-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 132–239（108 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；20 mM Tris pH 8.0 and 150 mM NaCl, 5mg/mL	Resolution 3.10 Å R-free 0.295
5VL3 CD22 d1-d3 in complex with therapeutic Fab Epratuzumab Deposited 2017-04-24	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Other combination Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 132–239（108 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；20 mM Tris pH 8.0 and 150 mM NaCl, 5mg/mL	Resolution 3.10 Å R-free 0.295
5VOB Crystal structure of HCMV Pentamer in complex with neutralizing antibody 8I21 Deposited 2017-05-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric	Chain H 126–241（116 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.2；293 K；10% (wt/vol) PEG400 10% isopropanol 2% (wt/vol) benzamidine 0.1M Tris pH 8.2	Resolution 3.02 Å R-free 0.237
5VOC Crystal structure of HCMV Pentamer in complex with neutralizing antibody 8I21 - Low resolution dataset for initial phasing by SAD Deposited 2017-05-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric	Chain H 126–241（116 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.2；293 K；10% (wt/vol) PEG400 10% isopropanol 2% (wt/vol) benzamidine 0.1M Tris pH 8.2	Resolution 3.99 Å R-free 0.276
5VOD Crystal structure of HCMV Pentamer in complex with neutralizing antibody 9I6 Deposited 2017-05-02	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 7 PDB declaration: heptameric	Chain H 132–241（110 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.2；293 K；10% (wt/vol) PEG methyl ether 500 0.1 M MES pH 6.2 0.00001 M phenol	Resolution 5.90 Å R-free 0.299
5VOD Crystal structure of HCMV Pentamer in complex with neutralizing antibody 9I6 Deposited 2017-05-02	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain H 132–241（110 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.2；293 K；10% (wt/vol) PEG methyl ether 500 0.1 M MES pH 6.2 0.00001 M phenol	Resolution 5.90 Å R-free 0.299
5VQM Clostridium difficile TcdB-GTD bound to PA41 Fab Deposited 2017-05-09	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain H 126–239（114 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；294 K；0.1 M Bis-Tris pH 5.5 1 M NaCl 11% PEG3350	Resolution 2.79 Å R-free 0.292
5VQM Clostridium difficile TcdB-GTD bound to PA41 Fab Deposited 2017-05-09	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 126–239（114 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；294 K；0.1 M Bis-Tris pH 5.5 1 M NaCl 11% PEG3350	Resolution 2.79 Å R-free 0.292
6AU5 Structure of cetuximab with aminoheptanoic acid-linked n-butylarginine meditope variant Deposited 2017-08-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 125–238（114 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M sodium citrate, pH 4.0, 1.6 M ammonium sulfate	Resolution 2.48 Å R-free 0.227
6AU5 Structure of cetuximab with aminoheptanoic acid-linked n-butylarginine meditope variant Deposited 2017-08-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 125–238（114 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M sodium citrate, pH 4.0, 1.6 M ammonium sulfate	Resolution 2.48 Å R-free 0.227
6AXP Structure of cetuximab with aminoheptanoic acid-linked n-octylarginine meditope variant Deposited 2017-09-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 125–238（114 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M sodium citrate pH 4.0, 1.6 M ammonium sulfate	Resolution 2.48 Å R-free 0.228
6AXP Structure of cetuximab with aminoheptanoic acid-linked n-octylarginine meditope variant Deposited 2017-09-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 125–238（114 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M sodium citrate pH 4.0, 1.6 M ammonium sulfate	Resolution 2.48 Å R-free 0.228
6AYN Structure of cetuximab with aminoheptanoic acid-linked N-(3-aminopropyl)-L-arginine meditope variant Deposited 2017-09-08	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 125–238（114 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M citrate pH 5, 1.6 M ammonium sulfate	Resolution 2.48 Å R-free 0.222
6AYN Structure of cetuximab with aminoheptanoic acid-linked N-(3-aminopropyl)-L-arginine meditope variant Deposited 2017-09-08	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 125–238（114 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M citrate pH 5, 1.6 M ammonium sulfate	Resolution 2.48 Å R-free 0.222
6AZK Structure of cetuximab with aminoheptanoic acid-linked N-(3-hydroxypropyl)-L-arginine meditope variant Deposited 2017-09-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 125–238（114 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M citrate pH 5, 1.8 M ammonium sulfate	Resolution 2.48 Å R-free 0.213
6AZK Structure of cetuximab with aminoheptanoic acid-linked N-(3-hydroxypropyl)-L-arginine meditope variant Deposited 2017-09-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 125–238（114 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M citrate pH 5, 1.8 M ammonium sulfate	Resolution 2.48 Å R-free 0.213
6AZL Structure of cetuximab with aminoheptanoic acid-linked N-carboxyethylarginine meditope variant Deposited 2017-09-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 125–238（114 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M citrate pH 5.5, 1.8 M ammonium sulfate	Resolution 2.48 Å R-free 0.216
6AZL Structure of cetuximab with aminoheptanoic acid-linked N-carboxyethylarginine meditope variant Deposited 2017-09-11	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 125–238（114 aa）	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M citrate pH 5.5, 1.8 M ammonium sulfate	Resolution 2.48 Å R-free 0.216
6B9Z Trastuzumab Fab v3 Deposited 2017-10-11	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 125–239（115 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Tris, pH 7.5, 24 mM NaCl, 15% PEG3350	Resolution 1.82 Å R-free 0.189
6BAE Trastuzumab Fab v3 in complex with CQFDLSTRRLKC Deposited 2017-10-12	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 125–239（115 aa）	Mutation：A175C, R217K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Tris pH 7.5, 24 mM NaCl, 15% PEG 3350	Resolution 2.14 Å R-free 0.224
6DCQ Ectodomain of full length, wild type HIV-1 glycoprotein clone PC64M18C043 in complex with PGT151 Fab Deposited 2018-05-08	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 Heteromer；Protein × 10 PDB declaration: decameric	Chain H 134–241（108 aa） Chain M 134–241（108 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 21	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；Detergent removed with Biobeads prior to grid freezing cryo-EM vitrification conditions Cryogen ETHANE；Blot force 0 Blot time 5 sec	Resolution 3.10 Å
6OKP B41 SOSIP.664 in complex with the silent-face antibody SF12 and V3-targeting antibody 10-1074 Deposited 2019-04-14	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 Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain K 138–243（106 aa） Chain M 126–243（118 aa） Chain O 126–243（118 aa） Chain Q 126–243（118 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；0 blot force, 3 second blot time, 3 uL sample added to freshly glow-discharged grids	Resolution 3.28 Å
6UTE Crystal structure of Z032 Fab in complex with WNV EDIII Deposited 2019-10-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 125–243（119 aa）	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M sodium bromide, 20% w/v polyethylene glycol 3,350	Resolution 2.90 Å R-free 0.264
6UTE Crystal structure of Z032 Fab in complex with WNV EDIII Deposited 2019-10-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 125–243（119 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M sodium bromide, 20% w/v polyethylene glycol 3,350	Resolution 2.90 Å R-free 0.264
6UTE Crystal structure of Z032 Fab in complex with WNV EDIII Deposited 2019-10-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 125–243（119 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M sodium bromide, 20% w/v polyethylene glycol 3,350	Resolution 2.90 Å R-free 0.264
6UTE Crystal structure of Z032 Fab in complex with WNV EDIII Deposited 2019-10-29	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 125–243（119 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M sodium bromide, 20% w/v polyethylene glycol 3,350	Resolution 2.90 Å R-free 0.264
6UTE Crystal structure of Z032 Fab in complex with WNV EDIII Deposited 2019-10-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain I 125–243（119 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M sodium bromide, 20% w/v polyethylene glycol 3,350	Resolution 2.90 Å R-free 0.264
6VTU DH717.1 Fab monomer in complex with man9 glycan Deposited 2020-02-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 137–237（101 aa） Fragment：FAB,FAB	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；100 mM sodium citrate, pH 5.0, 30% PEG4000	Resolution 2.61 Å R-free 0.224

27 other PDB entries and 47 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	S6B291_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 113–226； UniProt 129–242 Author chain H； PDBConstruct 113–226； UniProt 129–242

Fab light chain

Homo sapiens

UniProt P0DOX7

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain L； UniProt 109–214	Not recorded	Fab heavy chain × 1 （S6B291） Zika virus envelope protein DIII × 1 （A0A1I9ZK43）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5；295 K；10% isopropanol, 0.1M sodium citrate tribasic dihydrate pH 5.0, 26% PEG 400	Resolution 3.00 Å R-free 0.257
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain B； UniProt 109–214	Not recorded	Fab heavy chain × 1 （S6B291） Zika virus envelope protein DIII × 1 （A0A1I9ZK43） FLC CITRATE ANION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5；295 K；10% isopropanol, 0.1M sodium citrate tribasic dihydrate pH 5.0, 26% PEG 400	Resolution 3.00 Å R-free 0.257

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 5VIG	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4NM4 Crystal structure of broadly neutralizing antibody CR8043 Deposited 2013-11-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain L 115–214（100 aa）	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；20% PEG 6000, 0.1 M HEPES pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.65 Å R-free 0.232
4NM4 Crystal structure of broadly neutralizing antibody CR8043 Deposited 2013-11-14	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain M 115–214（100 aa）	Not recorded	PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；20% PEG 6000, 0.1 M HEPES pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.65 Å R-free 0.232
4NM8 Crystal structure of broadly neutralizing antibody CR8043 bound to H3 influenza hemagglutinin Deposited 2013-11-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 12 PDB declaration: dodecameric	Chain L 115–214（100 aa） Chain M 115–214（100 aa） Chain N 115–214（100 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；2.2 M ammonium sulfate, 0.1 M sodium acetate pH 5.5, 3% PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 4.00 Å R-free 0.292
5VIC Crystal structure of anti-Zika antibody Z004 bound to DENV-1 Envelope protein DIII Deposited 2017-04-14	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain L 109–214（106 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；295 K；0.1M sodium acetate trihydrate pH 4.5, 30% w/v PEG 1500	Resolution 3.00 Å R-free 0.286
5W1K JUNV GP1 CR1-10 Fab CR1-28 Fab complex Deposited 2017-06-03	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 109–212（104 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；pH 7.7；297 K；1.9 M AmSO4 pH 7.7	Resolution 3.99 Å R-free 0.288
5W1K JUNV GP1 CR1-10 Fab CR1-28 Fab complex Deposited 2017-06-03	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain F 109–212（104 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；pH 7.7；297 K；1.9 M AmSO4 pH 7.7	Resolution 3.99 Å R-free 0.288
5W1K JUNV GP1 CR1-10 Fab CR1-28 Fab complex Deposited 2017-06-03	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain K 109–212（104 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；pH 7.7；297 K；1.9 M AmSO4 pH 7.7	Resolution 3.99 Å R-free 0.288
5W1K JUNV GP1 CR1-10 Fab CR1-28 Fab complex Deposited 2017-06-03	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain S 109–212（104 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；pH 7.7；297 K；1.9 M AmSO4 pH 7.7	Resolution 3.99 Å R-free 0.288
6BF7 Cryo-EM structure of human insulin degrading enzyme in complex with FAB H11-E heavy chain, FAB H11-E light chain Deposited 2017-10-26	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 129–211（83 aa） Chain F 129–211（83 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE；The cryo grids were made using Spotiton	Resolution 6.50 Å
6BF9 Cryo-EM structure of human insulin degrading enzyme in complex with FAB H11-E heavy chain, FAB H11-E light chain Deposited 2017-10-26	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain D 109–211（103 aa） Chain F 109–211（103 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE；The cryo grids were made using Spotiton	Resolution 7.20 Å
6MSY Anti-HIV-1 Fab Fab 2G12 + Man4 re-refinement Deposited 2018-10-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain L 109–213（105 aa）	Not recorded	UNX UNKNOWN LIGAND × 8 ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.6；295 K；27% Peg 4000, 0.05M sodium acetate	Resolution 2.00 Å R-free 0.242
6MU3 Anti-HIV-1 Fab 2G12 + Man7 re-refinement Deposited 2018-10-22	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain K 110–213（104 aa） Chain L 110–213（104 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.6；295 K；20% Peg 4000, 0.2M sodium tartrate	Resolution 2.33 Å R-free 0.234
6MUB Anti-HIV-1 Fab 2G12 + Man5 re-refinement Deposited 2018-10-22	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain K 110–213（104 aa） Chain L 110–213（104 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；295 K；1.6M sodium/potassium phosphate	Resolution 2.50 Å R-free 0.280
6N2X Anti-HIV-1 Fab 2G12 + Man9 re-refinement Deposited 2018-11-14	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain K 109–213（105 aa） Chain L 109–213（105 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；295 K；25% Peg 400, 0.2M imidazole malate	Resolution 3.00 Å R-free 0.283
6N32 Anti-HIV-1 Fab 2G12 re-refinement Deposited 2018-11-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain L 109–213（105 aa） Chain M 109–213（105 aa）	Not recorded	SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；1.05M ammonium sulfate, 18% Peg 6000, 0.1M imidazole malate	Resolution 2.20 Å R-free 0.227
6N35 Anti-HIV-1 Fab 2G12 + Man1-2 re-refinement Deposited 2018-11-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain K 109–213（105 aa） Chain L 109–213（105 aa）	Not recorded	BEZ BENZOIC ACID × 1 GOL GLYCEROL × 1 MAN alpha-D-mannopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；2M Sodium/Potassium Phosphate	Resolution 1.75 Å R-free 0.238
6NQD Cryo-EM structure of T/F100 SOSIP.664 HIV-1 Env trimer in complex with 8ANC195 Fab Deposited 2019-01-21	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 Heteromer；Protein × 12 PDB declaration: dodecameric	Chain D 109–214（106 aa） Chain H 109–214（106 aa） Chain L 109–214（106 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 30	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
6UOE 3-25 Fab germline-reversion variant bound to an HCMV gB-derived peptide Deposited 2019-10-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain L 114–214（101 aa）	Not recorded	TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.1 M magnesium chloride, 13.4% PEG3350, 16.75% PEG400, 0.1 M Tris, pH 8.5	Resolution 1.80 Å R-free 0.186
6UTA Crystal structure of Z004 iGL Fab in complex with ZIKV EDIII Deposited 2019-10-29	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain L 109–214（106 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；% w/v tryptone, 0.001 M sodium azide, 0.05 M HEPES sodium pH 7.0, 20% w/v polyethylene glycol 3,350	Resolution 3.10 Å R-free 0.291
6UTA Crystal structure of Z004 iGL Fab in complex with ZIKV EDIII Deposited 2019-10-29	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 109–214（106 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；% w/v tryptone, 0.001 M sodium azide, 0.05 M HEPES sodium pH 7.0, 20% w/v polyethylene glycol 3,350	Resolution 3.10 Å R-free 0.291
6UTE Crystal structure of Z032 Fab in complex with WNV EDIII Deposited 2019-10-29	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 109–214（106 aa）	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M sodium bromide, 20% w/v polyethylene glycol 3,350	Resolution 2.90 Å R-free 0.264
6UTE Crystal structure of Z032 Fab in complex with WNV EDIII Deposited 2019-10-29	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 109–214（106 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M sodium bromide, 20% w/v polyethylene glycol 3,350	Resolution 2.90 Å R-free 0.264
6UTE Crystal structure of Z032 Fab in complex with WNV EDIII Deposited 2019-10-29	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 109–214（106 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M sodium bromide, 20% w/v polyethylene glycol 3,350	Resolution 2.90 Å R-free 0.264
6UTE Crystal structure of Z032 Fab in complex with WNV EDIII Deposited 2019-10-29	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 109–214（106 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M sodium bromide, 20% w/v polyethylene glycol 3,350	Resolution 2.90 Å R-free 0.264
6UTE Crystal structure of Z032 Fab in complex with WNV EDIII Deposited 2019-10-29	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain J 109–214（106 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M sodium bromide, 20% w/v polyethylene glycol 3,350	Resolution 2.90 Å R-free 0.264
8BBO SARS-CoV-2 Delta-RBD complexed with BA.2-36 Fab Deposited 2022-10-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain L 2–214（213 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；2% (v/v) PEG400, 0.1M imidazole pH7.0 and 24% (w/v) PEG MME 5000.	Resolution 2.75 Å R-free 0.252
8XKJ Ckappa domain of human immunoglobulin Deposited 2023-12-23	Different construct 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 110–213（104 aa） Fragment：Ckappa domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5；298 K；Ionic strength (raw mmCIF value) Not defined；Pressure 1 NMR sample composition 1.0 mM [U-13C; U-15N] protein, 5 mM Napi, 50 mM sodium chloride, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided

18 other PDB entries and 27 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	IGK_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 108–213； UniProt 109–214 Author chain L； PDBConstruct 108–213； UniProt 109–214

Zika virus envelope protein DIII

Zika virus

UniProt A0A1I9ZK43

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain Z； UniProt 589–697	Not recorded	Fab heavy chain × 1 （S6B291） Fab light chain × 1 （P0DOX7）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5；295 K；10% isopropanol, 0.1M sodium citrate tribasic dihydrate pH 5.0, 26% PEG 400	Resolution 3.00 Å R-free 0.257
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain G； UniProt 589–697	Not recorded	Fab heavy chain × 1 （S6B291） Fab light chain × 1 （P0DOX7） FLC CITRATE ANION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5；295 K；10% isopropanol, 0.1M sodium citrate tribasic dihydrate pH 5.0, 26% PEG 400	Resolution 3.00 Å R-free 0.257

Other States of the Same Protein in the Database

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	A0A1I9ZK43_ZIKV
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain G； PDBConstruct 2–110； UniProt 589–697 Author chain Z； PDBConstruct 2–110； UniProt 589–697

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	5vig
Deposition date deposition_date	2017-04-16
Structure title title	Crystal structure of anti-Zika antibody Z006 bound to Zika virus envelope protein DIII
Keywords keywords	antibody, Fab, Zika, Dengue, recurrent, neutralizing, immune system; IMMUNE SYSTEM
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	36.03 Å
Radius of gyration Rg (electron density) rg_electron	35.57 Å
Forward intensity I(0) i0	199283000.00
Molecular weight molecular_weight	112300.0 kDa
Excluded volume excluded_volume	139900 Å³
Envelope volume envelope_volume	184450 Å³
Hydration-shell volume shell_volume	44467 Å³
Envelope diameter envelope_diameter	116.6 Å
Shell Rg shell_rg	40.96 Å
Envelope Rg envelope_rg	35.14 Å
Shape Rg shape_rg	35.56 Å
Total Rg total_rg	35.97 Å
Total atoms total_atoms	7905
Residues n_residues	1036
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	114.5 Å
Rg (real space) rg_real	35.98 Å
Rg uncertainty (real space) rg_real_error	0.70 Å
I(0) (real space) i0_real	1.9930e+08
I(0) uncertainty (real space) i0_real_error	3.1640e+06
Rg (reciprocal space) rg_reciprocal	36.02 Å
I(0) (reciprocal space) i0_reciprocal	199300000.0000
Solution quality estimate total_estimate	0.9021
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	41.6 Å
Skewness Skewness skewness	0.224
Kurtosis Kurtosis kurtosis	-0.591
Angular range angular_range	— – 0.2200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	18690000.0000
Real-space data points n_real_points	45
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.959; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.851

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Fab heavy chain
Molecular weight formula_weight	25110.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H,A
Atom count atom_count	7905

EVQLLESGGGLVQPGGSLRLSCAASGFTFKNYAMAWVRQAPGKGLEWVSLLYNSEESTYYADSVKGRFTISRDNSKNTLFLQMNRLRVEDTAVYFCVRDRSNGWSSINLWGRGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVEPKSCDKTHHHHHH

来源 Source

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

Entity 2 Entity 2 polymer

Description description	Fab light chain
Molecular weight formula_weight	23411.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L,B

DIQMTQSPSTLSASVGDRVTMTCRASQTISGWLAWYQQKPGKAPKLLIYQASRLESGIPSRFSGSGSGTEFTLTISSLQPDDVATYYCQQYSTFWTFGLGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

来源 Source

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

Entity 3 Entity 3 polymer

Description description	Zika virus envelope protein DIII
Molecular weight formula_weight	11935.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Z,G

MRLKGVSYSLCTAAFTFTKIPAETLHGTVTVEVQYAGTDGPCKVPAQMAVDMQTLTPVGRLITANPVITESTENSKMMLELDPPFGDSYIVIGVGEKKITHHWHRSGSTI

来源 Source

来源生物 organism	Zika virus
通用名 common_name	ZIKV
NCBI Class编号 ncbi_taxonomy_id	64320
宿主生物 host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	CITRATE ANION
Molecular weight formula_weight	189.1 kDa
Source method src_method	syn
Copy count entity_count	1

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7. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d5viga_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d5vigb1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d5vigb2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d5vigg_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.18 — E set domains
Family Family family	b.1.18.4 — Class II viral fusion proteins C-terminal domain

Domain ID domain_id	d5vigh_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d5vigl1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d5vigl2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d5vigz_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.18 — E set domains
Family Family family	b.1.18.4 — Class II viral fusion proteins C-terminal domain

CATH v4.4 (10 domains)

Domain ID domain_id	5vigA01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5vigA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5vigB01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5vigB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5vigG00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	350 —

Domain ID domain_id	5vigH01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5vigH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5vigL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5vigL02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	5vigZ00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	350 —

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8. Citations (1)

▶

Unit-cell length a length_a	385.082 Å
Unit-cell length b length_b	385.082 Å
Unit-cell length c length_c	56.640 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	36

Space group space_group	H 3 2
Space-group number int_tables_number	155
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	29.749 Å
R factor r_factor	0.2142
R_work r_work	0.2119
R_free r_free	0.2569

fit	/app/data/saxs_computation/vi/5vig/5vig.fit
pddf	/app/data/pr_computation/vi/5vig/5vig.pr.out
profile	/app/data/saxs_computation/vi/5vig/5vig.dat

Crystal structure of anti-Zika antibody Z006 bound to Zika virus envelope protein DIII

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

Fab heavy chain

State in the Current Structure

Other States of the Same Protein in the Database

Fab light chain

State in the Current Structure

Other States of the Same Protein in the Database

Zika virus envelope protein DIII

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

7. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (8 domains)

CATH v4.4 (10 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)