6bpa

Plasmodium vivax reticulocyte binding protein 2b (PvRBP2b) bound to monoclonal antibody 3E9

Method: X-RAY DIFFRACTION D_max: 127.2 Å Quality: GOOD

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

Reticulocyte binding protein 2, putative

Plasmodium vivax (strain Salvador I)

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 A； UniProt 15–316	Not recorded	Monoclonal antibody 3E9 Fab heavy chain × 1 Monoclonal antibody 3E9 Fab light chain × 1 BR BROMIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；295 K；0.2 M KBr, 15% (w/v) PEG 4,000 and 0.05 M sodium citrate/citric acid	Resolution 2.53 Å R-free 0.225
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain D； UniProt 15–316	Not recorded	Monoclonal antibody 3E9 Fab heavy chain × 1 Monoclonal antibody 3E9 Fab light chain × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；295 K；0.2 M KBr, 15% (w/v) PEG 4,000 and 0.05 M sodium citrate/citric acid	Resolution 2.53 Å R-free 0.225

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 6BPA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5W53 Crystal structure of the erythrocyte-binding domain from Plasmodium vivax reticulocyte-binding protein 2b (PvRBP2b) Deposited 2017-06-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 15–316（302 aa） Fragment：ERYTHROCYTE-BINDING DOMAIN (RESIDUES 169-470)	Not recorded	SCN THIOCYANATE ION × 3 K POTASSIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；22% W/V PEG3350, 200 MM POTASSIUM THIOCYANATE, 100 MM BIS-TRIS-HCL, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K	Resolution 1.71 Å R-free 0.188
5W53 Crystal structure of the erythrocyte-binding domain from Plasmodium vivax reticulocyte-binding protein 2b (PvRBP2b) Deposited 2017-06-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 15–316（302 aa） Fragment：ERYTHROCYTE-BINDING DOMAIN (RESIDUES 169-470)	Not recorded	SCN THIOCYANATE ION × 2 K POTASSIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；22% W/V PEG3350, 200 MM POTASSIUM THIOCYANATE, 100 MM BIS-TRIS-HCL, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K	Resolution 1.71 Å R-free 0.188
6BPC Plasmodium vivax reticulocyte binding protein 2b (PvRBP2b) bound to monoclonal antibody 4F7 Deposited 2017-11-22	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 15–316（302 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.2 M trisodium citrate and 20% (w/v) PEG 3,350	Resolution 2.66 Å R-free 0.215
6BPC Plasmodium vivax reticulocyte binding protein 2b (PvRBP2b) bound to monoclonal antibody 4F7 Deposited 2017-11-22	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 15–316（302 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.2 M trisodium citrate and 20% (w/v) PEG 3,350	Resolution 2.66 Å R-free 0.215
6BPE Plasmodium vivax reticulocyte binding protein 2b (PvRBP2b) bound to monoclonal antibody 6H1 Deposited 2017-11-22	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 15–316（302 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.2 M (NH4)2SO4, 20% (w/v) PEG 3,350	Resolution 3.34 Å R-free 0.367
6BPE Plasmodium vivax reticulocyte binding protein 2b (PvRBP2b) bound to monoclonal antibody 6H1 Deposited 2017-11-22	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 15–316（302 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.2 M (NH4)2SO4, 20% (w/v) PEG 3,350	Resolution 3.34 Å R-free 0.367
6BPE Plasmodium vivax reticulocyte binding protein 2b (PvRBP2b) bound to monoclonal antibody 6H1 Deposited 2017-11-22	Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 15–316（302 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.2 M (NH4)2SO4, 20% (w/v) PEG 3,350	Resolution 3.34 Å R-free 0.367
6BPE Plasmodium vivax reticulocyte binding protein 2b (PvRBP2b) bound to monoclonal antibody 6H1 Deposited 2017-11-22	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain J 15–316（302 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.2 M (NH4)2SO4, 20% (w/v) PEG 3,350	Resolution 3.34 Å R-free 0.367
6D03 Cryo-EM structure of a Plasmodium vivax invasion complex essential for entry into human reticulocytes; one molecule of parasite ligand. Deposited 2018-04-10	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain E 2–815（814 aa）	Not recorded	CA CALCIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 FE FE (III) ION × 4 CO3 CARBONATE ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.68 Å
6D04 Cryo-EM structure of a Plasmodium vivax invasion complex essential for entry into human reticulocytes; two molecules of parasite ligand, subclass 1. Deposited 2018-04-10	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 × 6 PDB declaration: hexameric	Chain E 1–815（815 aa） Chain F 1–815（815 aa）	Not recorded	CA CALCIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 FE FE (III) ION × 4 CO3 CARBONATE ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.74 Å
6D05 Cryo-EM structure of a Plasmodium vivax invasion complex essential for entry into human reticulocytes; two molecules of parasite ligand, subclass 2. Deposited 2018-04-10	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 × 6 PDB declaration: hexameric	Chain E 1–815（815 aa） Chain F 1–815（815 aa）	Not recorded	CA CALCIUM ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 FE FE (III) ION × 4 CO3 CARBONATE ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
6WM9 Plasmodium vivax reticulocyte binding protein 2b (PvRBP2b) bound to human monoclonal antibody 237235 Deposited 2020-04-20	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 15–316（302 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.1 M magnesium formate, 15% (w/v) PEG 3,350	Resolution 2.45 Å R-free 0.279
6WM9 Plasmodium vivax reticulocyte binding protein 2b (PvRBP2b) bound to human monoclonal antibody 237235 Deposited 2020-04-20	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 15–316（302 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295 K；0.1 M magnesium formate, 15% (w/v) PEG 3,350	Resolution 2.45 Å R-free 0.279
6WN1 Plasmodium vivax reticulocyte binding protein 2b (PvRBP2b) bound to human monoclonal antibody 241242 Deposited 2020-04-22	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 15–316（302 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；0.4 M sodium thiocyanate, 17% (w/v) PEG 3,350	Resolution 3.15 Å R-free 0.283
6WN1 Plasmodium vivax reticulocyte binding protein 2b (PvRBP2b) bound to human monoclonal antibody 241242 Deposited 2020-04-22	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 15–316（302 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；0.4 M sodium thiocyanate, 17% (w/v) PEG 3,350	Resolution 3.15 Å R-free 0.283
6WNO Plasmodium vivax reticulocyte binding protein 2b (PvRBP2b) bound to human monoclonal antibody 243244 Deposited 2020-04-23	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 15–316（302 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；0.2 M trimethylamine N-oxide, 0.1 M Tris chloride pH 8.5, 20% (w/v) PEG monomethyl ether 2,000	Resolution 3.35 Å R-free 0.283
6WNO Plasmodium vivax reticulocyte binding protein 2b (PvRBP2b) bound to human monoclonal antibody 243244 Deposited 2020-04-23	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 15–316（302 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；295 K；0.2 M trimethylamine N-oxide, 0.1 M Tris chloride pH 8.5, 20% (w/v) PEG monomethyl ether 2,000	Resolution 3.35 Å R-free 0.283
6WOZ Plasmodium vivax reticulocyte binding protein 2b (PvRBP2b) bound to human monoclonal antibody 251249 Deposited 2020-04-26	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain J 15–316（302 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；0.2 M DL-malate-imidazole pH 6.0, 15% (w/v) PEG 4,000	Resolution 2.90 Å R-free 0.258
6WOZ Plasmodium vivax reticulocyte binding protein 2b (PvRBP2b) bound to human monoclonal antibody 251249 Deposited 2020-04-26	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 15–316（302 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；0.2 M DL-malate-imidazole pH 6.0, 15% (w/v) PEG 4,000	Resolution 2.90 Å R-free 0.258
6WOZ Plasmodium vivax reticulocyte binding protein 2b (PvRBP2b) bound to human monoclonal antibody 251249 Deposited 2020-04-26	Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 15–316（302 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；0.2 M DL-malate-imidazole pH 6.0, 15% (w/v) PEG 4,000	Resolution 2.90 Å R-free 0.258
6WOZ Plasmodium vivax reticulocyte binding protein 2b (PvRBP2b) bound to human monoclonal antibody 251249 Deposited 2020-04-26	Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 15–316（302 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；0.2 M DL-malate-imidazole pH 6.0, 15% (w/v) PEG 4,000	Resolution 2.90 Å R-free 0.258
6WQO Plasmodium vivax reticulocyte binding protein 2b (PvRBP2b) bound to human monoclonal antibody 283284 Deposited 2020-04-29	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 15–316（302 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；0.3 M ammonium nitrate, 0.1 M sodium HEPES pH 7.0, 26% (w/v) PEG 2,000	Resolution 3.15 Å R-free 0.305
6WQO Plasmodium vivax reticulocyte binding protein 2b (PvRBP2b) bound to human monoclonal antibody 283284 Deposited 2020-04-29	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 15–316（302 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；0.3 M ammonium nitrate, 0.1 M sodium HEPES pH 7.0, 26% (w/v) PEG 2,000	Resolution 3.15 Å R-free 0.305
6WTU Plasmodium vivax reticulocyte binding protein 2b (PvRBP2b) bound to human monoclonal antibody 273264 Deposited 2020-05-04	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 15–316（302 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；0.1 M sodium cacodylate pH 6.0, 0.1 M magnesium chloride, 15 % (w/v) PEG 4,000	Resolution 2.55 Å R-free 0.255
6WTU Plasmodium vivax reticulocyte binding protein 2b (PvRBP2b) bound to human monoclonal antibody 273264 Deposited 2020-05-04	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain J 15–316（302 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；0.1 M sodium cacodylate pH 6.0, 0.1 M magnesium chloride, 15 % (w/v) PEG 4,000	Resolution 2.55 Å R-free 0.255
6WTU Plasmodium vivax reticulocyte binding protein 2b (PvRBP2b) bound to human monoclonal antibody 273264 Deposited 2020-05-04	Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 15–316（302 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；0.1 M sodium cacodylate pH 6.0, 0.1 M magnesium chloride, 15 % (w/v) PEG 4,000	Resolution 2.55 Å R-free 0.255
6WTU Plasmodium vivax reticulocyte binding protein 2b (PvRBP2b) bound to human monoclonal antibody 273264 Deposited 2020-05-04	Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 15–316（302 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；0.1 M sodium cacodylate pH 6.0, 0.1 M magnesium chloride, 15 % (w/v) PEG 4,000	Resolution 2.55 Å R-free 0.255
6WTV Plasmodium vivax reticulocyte binding protein 2b (PvRBP2b) bound to human monoclonal antibody 258259 Deposited 2020-05-04	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 15–316（302 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；0.4 M ammonium nitrate, 18% (w/v) PEG 3,350	Resolution 3.05 Å R-free 0.277
6WTV Plasmodium vivax reticulocyte binding protein 2b (PvRBP2b) bound to human monoclonal antibody 258259 Deposited 2020-05-04	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 15–316（302 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；0.4 M ammonium nitrate, 18% (w/v) PEG 3,350	Resolution 3.05 Å R-free 0.277
6WTV Plasmodium vivax reticulocyte binding protein 2b (PvRBP2b) bound to human monoclonal antibody 258259 Deposited 2020-05-04	Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain J 15–316（302 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；0.4 M ammonium nitrate, 18% (w/v) PEG 3,350	Resolution 3.05 Å R-free 0.277
6WTV Plasmodium vivax reticulocyte binding protein 2b (PvRBP2b) bound to human monoclonal antibody 258259 Deposited 2020-05-04	Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 15–316（302 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；0.4 M ammonium nitrate, 18% (w/v) PEG 3,350	Resolution 3.05 Å R-free 0.277
6WTY Plasmodium vivax reticulocyte binding protein 2b (PvRBP2b) bound to human monoclonal antibody 253245 Deposited 2020-05-04	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 15–316（302 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；295 K；0.2 M sodium dihydrogen phosphate pH 4.0, 16% (w/v) PEG 3,350	Resolution 3.48 Å R-free 0.301
6WTY Plasmodium vivax reticulocyte binding protein 2b (PvRBP2b) bound to human monoclonal antibody 253245 Deposited 2020-05-04	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain J 15–316（302 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；295 K；0.2 M sodium dihydrogen phosphate pH 4.0, 16% (w/v) PEG 3,350	Resolution 3.48 Å R-free 0.301
6WTY Plasmodium vivax reticulocyte binding protein 2b (PvRBP2b) bound to human monoclonal antibody 253245 Deposited 2020-05-04	Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 15–316（302 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；295 K；0.2 M sodium dihydrogen phosphate pH 4.0, 16% (w/v) PEG 3,350	Resolution 3.48 Å R-free 0.301
6WTY Plasmodium vivax reticulocyte binding protein 2b (PvRBP2b) bound to human monoclonal antibody 253245 Deposited 2020-05-04	Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 15–316（302 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；295 K；0.2 M sodium dihydrogen phosphate pH 4.0, 16% (w/v) PEG 3,350	Resolution 3.48 Å R-free 0.301

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

View Construct and Data Evidence

UniProt name	A5K736_PLAVS
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–307； UniProt 15–316 Author chain D； PDBConstruct 6–307； UniProt 15–316

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	6bpa
Deposition date deposition_date	2017-11-22
Structure title title	Plasmodium vivax reticulocyte binding protein 2b (PvRBP2b) bound to monoclonal antibody 3E9
Keywords keywords	Plasmodium vivax, invasion, malaria, antibody complex, CELL INVASION; CELL INVASION
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	42.73 Å
Radius of gyration Rg (electron density) rg_electron	42.27 Å
Forward intensity I(0) i0	396185000.00
Molecular weight molecular_weight	163520.0 kDa
Excluded volume excluded_volume	204840 Å³
Envelope volume envelope_volume	285470 Å³
Hydration-shell volume shell_volume	57980 Å³
Envelope diameter envelope_diameter	127.0 Å
Shell Rg shell_rg	46.07 Å
Envelope Rg envelope_rg	41.26 Å
Shape Rg shape_rg	42.23 Å
Total Rg total_rg	42.62 Å
Total atoms total_atoms	11517
Residues n_residues	1448
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	127.2 Å
Rg (real space) rg_real	42.58 Å
Rg uncertainty (real space) rg_real_error	0.87 Å
I(0) (real space) i0_real	3.9620e+08
I(0) uncertainty (real space) i0_real_error	7.3990e+06
Rg (reciprocal space) rg_reciprocal	42.73 Å
I(0) (reciprocal space) i0_reciprocal	396200000.0000
Solution quality estimate total_estimate	0.8902
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	48.1 Å
Skewness Skewness skewness	0.078
Kurtosis Kurtosis kurtosis	-0.782
Angular range angular_range	— – 0.1850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	18070000.0000
Real-space data points n_real_points	38
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.982; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.624

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Reticulocyte binding protein 2, putative
Molecular weight formula_weight	36519.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	12059

GAMGSTNTTDNIDYFDISDESNYYLISQLRPHFSNIYFFDEFKRYASYHTEIKRYEDIHKTKVNSLLNEASRAIGICNRAKNTVKGLINILENPQKFKTQRESYDVKLRQYEEKKEAFRGCLLNKNRKNLDQIKKINNEIRDLLEKLKCSQDCQTNVYFDMIKIYLVDFKKMPYENYDTFIKQYKNSYLSGVDMIRKIEKQIDNPVTINAIKFTQKEMGYIIDRFEYHLQKVKHSIDQVTALSDGVKPKQVTKNRLKEYYFNIGNYYSIFKFGKDSLNMLNKALIHKEKIVHNLLGELFGHLEERIS

来源 Source

来源生物 organism	Plasmodium vivax (strain Salvador I)
NCBI Class编号 ncbi_taxonomy_id	126793
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Monoclonal antibody 3E9 Fab heavy chain
Molecular weight formula_weight	27243.8 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

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

MKCSWIIFFLMAVVTGVNSEVQLQQSGAELVKPGASVKLSCTASGFNIKDHFMHWVKQRTAQGLEWIGRIDPEDGETKYAPKFQGTATITADTSSNTAYLQLSSLTSEDTAVYYCARSGSVSSPWFAYWGQGTLVTVSAAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRGPTIKPCPPCKCPAPNS

Entity 3 Entity 3 polymer

Description description	Monoclonal antibody 3E9 Fab light chain
Molecular weight formula_weight	26030.1 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

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

MTMFSLALLLSLLLLCVSDSRAETTVTQSPASLSMALGEKVTIRCITSTDIDDDLNWYQLKPGEPPKLLISEGNTLRPGVPSRFSSSGYGTDFVFTIENMLSEDVADYYCLQSDNLPLTFGAGTKLELKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Entity 4 Entity 4 non-polymer

Description description	BROMIDE ION
Molecular weight formula_weight	79.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	542

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d6bpab_
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	d6bpac1
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	d6bpac2
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	d6bpae_
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	d6bpaf1
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	d6bpaf2
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

CATH v4.4 (6 domains)

Domain ID domain_id	6bpaB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6bpaC01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6bpaC02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6bpaE02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6bpaF01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	6bpaF02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	59.070 Å
Unit-cell length b length_b	177.100 Å
Unit-cell length c length_c	178.620 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

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

Resolution resolution	2.530 Å
Low-resolution limit resolution_low	56.051 Å
R factor r_factor	0.1947
R_work r_work	0.1942
R_free r_free	0.2246

fit	/app/data/saxs_computation/bp/6bpa/6bpa.fit
pddf	/app/data/pr_computation/bp/6bpa/6bpa.pr.out
profile	/app/data/saxs_computation/bp/6bpa/6bpa.dat

Plasmodium vivax reticulocyte binding protein 2b (PvRBP2b) bound to monoclonal antibody 3E9

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

Reticulocyte binding protein 2, putative

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)