2qvd

Identification of a potent anti-inflammatory agent from the natural extract of plant Cardiospermun helicacabum: Crystal structure of the complex of phospholipase A2 with Benzo(g)-1,3-benzodioxolo(5,6-a)quinolizinium, 5,6-dihydro-9,10-dimethoxy at 1.93 A resolution

Method: X-RAY DIFFRACTION D_max: 52.6 Å Quality: GOOD

▼

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

Phospholipase A2 VRV-PL-VIIIa

OrganismNot specified

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–121	Not recorded	BER BERBERINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.8；298 K；50mm Ammonium acetate, 0.2M ammonium sulphate, 30%PEG 4000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.93 Å R-free 0.224

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 2QVD	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1CL5 CRYSTAL STRUCTURE OF PHOSPHOLIPASE A2 FROM DABOIA RUSSELLI PULCHELLA Deposited 1999-05-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–39（39 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；PROTEIN WAS CRYSTALLISED FROM 1.2 AMMONIUM SULPHATE BUFFER WITH 20MM SODIUM CACODYLATE, 2MM CALCIUM CHLORIDE AND 3% DIOXANE, pH 7.0	Resolution 2.45 Å R-free 0.267
1CL5 CRYSTAL STRUCTURE OF PHOSPHOLIPASE A2 FROM DABOIA RUSSELLI PULCHELLA Deposited 1999-05-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–39（39 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；PROTEIN WAS CRYSTALLISED FROM 1.2 AMMONIUM SULPHATE BUFFER WITH 20MM SODIUM CACODYLATE, 2MM CALCIUM CHLORIDE AND 3% DIOXANE, pH 7.0	Resolution 2.45 Å R-free 0.267
1FB2 STRUCTURE OF PHOSPHOLIPASE A2 FROM DABOIA RUSSELLI PULCHELLA AT 1.95 Deposited 2000-07-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–50（50 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；20mM Sodium Cacodylate, 1.4M Ammonium Sulphate, 4mM Calcium Chloride, 3% Dioxane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.95 Å R-free 0.272
1FB2 STRUCTURE OF PHOSPHOLIPASE A2 FROM DABOIA RUSSELLI PULCHELLA AT 1.95 Deposited 2000-07-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–50（50 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；20mM Sodium Cacodylate, 1.4M Ammonium Sulphate, 4mM Calcium Chloride, 3% Dioxane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.95 Å R-free 0.272
1FV0 FIRST STRUCTURAL EVIDENCE OF THE INHIBITION OF PHOSPHOLIPASE A2 BY ARISTOLOCHIC ACID: CRYSTAL STRUCTURE OF A COMPLEX FORMED BETWEEN PHOSPHOLIPASE A2 AND ARISTOLOCHIC ACID Deposited 2000-09-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–50（50 aa）	Not recorded	SO4 SULFATE ION × 2 ACT ACETATE ION × 1 9AR 9-HYDROXY ARISTOLOCHIC ACID × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；20mM Sodium cacodylate, 1.4M Ammonium sulfate, 4mM Calcium chloride, 3% dioxane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.70 Å R-free 0.201
1FV0 FIRST STRUCTURAL EVIDENCE OF THE INHIBITION OF PHOSPHOLIPASE A2 BY ARISTOLOCHIC ACID: CRYSTAL STRUCTURE OF A COMPLEX FORMED BETWEEN PHOSPHOLIPASE A2 AND ARISTOLOCHIC ACID Deposited 2000-09-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–50（50 aa）	Not recorded	SO4 SULFATE ION × 2 GOL GLYCEROL × 1 DIO 1,4-DIETHYLENE DIOXIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；20mM Sodium cacodylate, 1.4M Ammonium sulfate, 4mM Calcium chloride, 3% dioxane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.70 Å R-free 0.201
1FV0 FIRST STRUCTURAL EVIDENCE OF THE INHIBITION OF PHOSPHOLIPASE A2 BY ARISTOLOCHIC ACID: CRYSTAL STRUCTURE OF A COMPLEX FORMED BETWEEN PHOSPHOLIPASE A2 AND ARISTOLOCHIC ACID Deposited 2000-09-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–50（50 aa） Chain B 1–50（50 aa）	Not recorded	SO4 SULFATE ION × 8 ACT ACETATE ION × 2 9AR 9-HYDROXY ARISTOLOCHIC ACID × 2 GOL GLYCEROL × 4 DIO 1,4-DIETHYLENE DIOXIDE × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；20mM Sodium cacodylate, 1.4M Ammonium sulfate, 4mM Calcium chloride, 3% dioxane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.70 Å R-free 0.201
1JQ9 Crystal structure of a complex formed between phospholipase A2 from Daboia russelli pulchella and a designed pentapeptide Phe-Leu-Ser-Tyr-Lys at 1.8 resolution Deposited 2001-08-04	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–121（121 aa）	Not recorded	ACY ACETIC ACID × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；20mM Sodium cacodylate, 1.4M Ammonium sulfate, 4mM Calcium chloride, 3% dioxane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.80 Å R-free 0.225
1JQ9 Crystal structure of a complex formed between phospholipase A2 from Daboia russelli pulchella and a designed pentapeptide Phe-Leu-Ser-Tyr-Lys at 1.8 resolution Deposited 2001-08-04	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–121（121 aa）	Not recorded	ACY ACETIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；20mM Sodium cacodylate, 1.4M Ammonium sulfate, 4mM Calcium chloride, 3% dioxane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.80 Å R-free 0.225
1JQ9 Crystal structure of a complex formed between phospholipase A2 from Daboia russelli pulchella and a designed pentapeptide Phe-Leu-Ser-Tyr-Lys at 1.8 resolution Deposited 2001-08-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–121（121 aa） Chain B 1–121（121 aa）	Not recorded	ACY ACETIC ACID × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；20mM Sodium cacodylate, 1.4M Ammonium sulfate, 4mM Calcium chloride, 3% dioxane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.80 Å R-free 0.225
1JQ9 Crystal structure of a complex formed between phospholipase A2 from Daboia russelli pulchella and a designed pentapeptide Phe-Leu-Ser-Tyr-Lys at 1.8 resolution Deposited 2001-08-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–121（121 aa） Chain B 1–121（121 aa）	Not recorded	ACY ACETIC ACID × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；20mM Sodium cacodylate, 1.4M Ammonium sulfate, 4mM Calcium chloride, 3% dioxane, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.80 Å R-free 0.225
1KPM First Structural Evidence of a Specific Inhibition of Phospholipase A2 by Vitamin E and its Implications in Inflammation: Crystal Structure of the Complex Formed between Phospholipase A2 and Vitamin E at 1.8 A Resolution. Deposited 2002-01-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–50（50 aa）	Not recorded	VIT VITAMIN E × 1 ACY ACETIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；20mM Sodium cacodylate, 1.4M Ammonium sulfate, 4mM Calcium chloride, 3% dioxane, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.80 Å R-free 0.228
1KPM First Structural Evidence of a Specific Inhibition of Phospholipase A2 by Vitamin E and its Implications in Inflammation: Crystal Structure of the Complex Formed between Phospholipase A2 and Vitamin E at 1.8 A Resolution. Deposited 2002-01-01	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–50（50 aa）	Not recorded	ACY ACETIC ACID × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；20mM Sodium cacodylate, 1.4M Ammonium sulfate, 4mM Calcium chloride, 3% dioxane, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.80 Å R-free 0.228
1OXL INHIBITION OF PHOSPHOLIPASE A2 (PLA2) BY (2-CARBAMOYLMETHYL-5-PROPYL-OCTAHYDRO-INDOL-7-YL)-ACETIC ACID (INDOLE): CRYSTAL STRUCTURE OF THE COMPLEX FORMED BETWEEN PLA2 FROM RUSSELL'S VIPER AND INDOLE AT 1.8 RESOLUTION Deposited 2003-04-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–121（121 aa） Chain B 1–121（121 aa）	Not recorded	IDA (2-CARBAMOYLMETHYL-5-PROPYL-OCTAHYDRO-INDOL-7-YL)ACETIC ACID × 1 CO3 CARBONATE ION × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；290 K；1.2 Ammonium sulphate buffer with 20mm sodium cacodylate, 50mm calcium chloride, 3% dioxane, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 1.80 Å R-free 0.238
1OXL INHIBITION OF PHOSPHOLIPASE A2 (PLA2) BY (2-CARBAMOYLMETHYL-5-PROPYL-OCTAHYDRO-INDOL-7-YL)-ACETIC ACID (INDOLE): CRYSTAL STRUCTURE OF THE COMPLEX FORMED BETWEEN PLA2 FROM RUSSELL'S VIPER AND INDOLE AT 1.8 RESOLUTION Deposited 2003-04-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–121（121 aa） Chain B 1–121（121 aa）	Not recorded	IDA (2-CARBAMOYLMETHYL-5-PROPYL-OCTAHYDRO-INDOL-7-YL)ACETIC ACID × 2 CO3 CARBONATE ION × 4 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；290 K；1.2 Ammonium sulphate buffer with 20mm sodium cacodylate, 50mm calcium chloride, 3% dioxane, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 1.80 Å R-free 0.238
1OXL INHIBITION OF PHOSPHOLIPASE A2 (PLA2) BY (2-CARBAMOYLMETHYL-5-PROPYL-OCTAHYDRO-INDOL-7-YL)-ACETIC ACID (INDOLE): CRYSTAL STRUCTURE OF THE COMPLEX FORMED BETWEEN PLA2 FROM RUSSELL'S VIPER AND INDOLE AT 1.8 RESOLUTION Deposited 2003-04-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–121（121 aa） Chain B 1–121（121 aa）	Not recorded	IDA (2-CARBAMOYLMETHYL-5-PROPYL-OCTAHYDRO-INDOL-7-YL)ACETIC ACID × 1 CO3 CARBONATE ION × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；290 K；1.2 Ammonium sulphate buffer with 20mm sodium cacodylate, 50mm calcium chloride, 3% dioxane, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 1.80 Å R-free 0.238
1OXL INHIBITION OF PHOSPHOLIPASE A2 (PLA2) BY (2-CARBAMOYLMETHYL-5-PROPYL-OCTAHYDRO-INDOL-7-YL)-ACETIC ACID (INDOLE): CRYSTAL STRUCTURE OF THE COMPLEX FORMED BETWEEN PLA2 FROM RUSSELL'S VIPER AND INDOLE AT 1.8 RESOLUTION Deposited 2003-04-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–121（121 aa） Chain B 1–121（121 aa）	Not recorded	IDA (2-CARBAMOYLMETHYL-5-PROPYL-OCTAHYDRO-INDOL-7-YL)ACETIC ACID × 1 CO3 CARBONATE ION × 2 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；290 K；1.2 Ammonium sulphate buffer with 20mm sodium cacodylate, 50mm calcium chloride, 3% dioxane, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K	Resolution 1.80 Å R-free 0.238
1OYF Crystal Structure of Russelles viper (Daboia russellii pulchella) phospholipase A2 in a complex with venom 6-methyl heptanol Deposited 2003-04-04	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–121（121 aa）	Not recorded	SO4 SULFATE ION × 1 MHN 6-METHYLHEPTAN-1-OL × 2 ACY ACETIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1M Cacodylate buffer, 0.2M Ammonoum Sulphate, 15% PEG8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.45 Å R-free 0.235
1Q6V First crystal structure of a C49 monomer PLA2 from the venom of Daboia russelli pulchella at 1.8 A resolution Deposited 2003-08-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–121（121 aa） Fragment：Phospholipase A2	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；30%PEG4000, 0.2M Ammonium Sulphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.86 Å R-free 0.208
1Q7A Crystal structure of the complex formed between russell's viper phospholipase A2 and an antiinflammatory agent oxyphenbutazone at 1.6A resolution Deposited 2003-08-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–121（121 aa） Fragment：Phospholipase A2	Not recorded	SO4 SULFATE ION × 2 OPB 4-BUTYL-1-(4-HYDROXYPHENYL)-2-PHENYLPYRAZOLIDINE-3,5-DIONE × 1 MOH METHANOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；30% PEG 4000, 0.2M ammonium sulphate,30% Methanol, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.60 Å R-free 0.213
1SQZ Design of specific inhibitors of Phopholipase A2: Crystal structure of the complex formed between Group II Phopholipase A2 and a designed peptide Dehydro-Ile-Ala-Arg-Ser at 1.2A resolution Deposited 2004-03-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–121（121 aa）	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；297 K；0.2M Ammonium sulphate,50% PEG, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 1.20 Å R-free 0.217
1SV3 Structure of the complex formed between Phospholipase A2 and 4-methoxybenzoic acid at 1.3A resolution. Deposited 2004-03-27	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–50（50 aa）	Not recorded	SO4 SULFATE ION × 5 ANN 4-METHOXYBENZOIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；297 K；0.2M Ammonium sulphate, 50% PEG, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 1.35 Å R-free 0.243
1SV9 Crystal structure of the complex formed between groupII phospholipase A2 and anti-inflammatory agent 2-[(2,6-Dichlorophenyl)amino] benzeneacetic acid at 2.7A resolution Deposited 2004-03-29	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–121（121 aa）	Not recorded	DIF 2-[2,6-DICHLOROPHENYL)AMINO]BENZENEACETIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；297 K；0.2M Ammonium sulphate, 50% PEG, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 2.71 Å R-free 0.238
1SXK Crystal Structure of a complex formed between phospholipase A2 and a non-specific anti-inflammatory amino salicylic acid at 1.2 A resolution Deposited 2004-03-31	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–121（121 aa）	Not recorded	SO4 SULFATE ION × 4 BHA 2-HYDROXY-4-AMINOBENZOIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；297 K；0.2M ammonium sulphate, 50% PEG, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 1.21 Å R-free 0.188
1TDV Non-specific binding to phospholipase A2:Crystal structure of the complex of PLA2 with a designed peptide Tyr-Trp-Ala-Ala-Ala-Ala at 1.7A resolution Deposited 2004-05-24	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–121（121 aa）	Not recorded	SO4 SULFATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.2M AMMONIUM SULPHATE, 30% PEG, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.70 Å R-free 0.206
1TG1 Crystal Structure of the complex formed between russells viper phospholipase A2 and a designed peptide inhibitor PHQ-Leu-Val-Arg-Tyr at 1.2A resolution Deposited 2004-05-28	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–121（121 aa）	Not recorded	SO4 SULFATE ION × 3 ACY ACETIC ACID × 1 MOH METHANOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.2M AMMONIUM SULPHATE, 30% PEG, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.25 Å R-free 0.197
1TG4 Design of specific inhibitors of groupII phospholipase A2(PLA2): Crystal structure of the complex formed between russells viper PLA2 and designed peptide Phe-Leu-Ala-Tyr-Lys at 1.7A resolution Deposited 2004-05-28	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–121（121 aa）	Not recorded	SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.2M AMMONIUM SULPHATE, 30% PEG, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.70 Å R-free 0.196
1TGM Crystal structure of a complex formed between group II phospholipase A2 and aspirin at 1.86 A resolution Deposited 2004-05-28	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–121（121 aa）	Not recorded	AIN 2-(ACETYLOXY)BENZOIC ACID × 1 CA CALCIUM ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；Polyethylene glycol, ammonium sulphate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.86 Å R-free 0.224
1TH6 Crystal structure of phospholipase A2 in complex with atropine at 1.23A resolution Deposited 2004-06-01	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–121（121 aa）	Not recorded	OIN (1R,5S)-8-METHYL-8-AZABICYCLO[3.2.1]OCT-3-YL (2R)-3-HYDROXY-2-PHENYLPROPANOATE × 1 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.2M ammonium sulphate, 30% PEG 4000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.23 Å R-free 0.204
1TJ9 Structure of the complexed formed between group II phospholipase A2 and a rationally designed tetra peptide,Val-Ala-Arg-Ser at 1.1A resolution Deposited 2004-06-03	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–121（121 aa）	Not recorded	SO4 SULFATE ION × 5 ACY ACETIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.2M AMMONIUM SULPHATE, 30% PEG, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.10 Å R-free 0.209
1TJK Crystal structure of the complex formed between group II phospholipase A2 with a designed pentapeptide, Phe- Leu- Ser- Thr- Lys at 1.2 A resolution Deposited 2004-06-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–121（121 aa）	Not recorded	SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；Ammonium Sulphate, Polyethylene glycol, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.25 Å R-free 0.203
1TK4 Crystal structure of russells viper phospholipase A2 in complex with a specifically designed tetrapeptide Ala-Ile-Arg-Ser at 1.1 A resolution Deposited 2004-06-08	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–121（121 aa）	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.2M AMMONIUM SULPHATE, 30% PEG , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.10 Å R-free 0.185
1TP2 Crystal structure of the complex of group II phospholipaseA2 dimer with a fatty acid tridecanoic acid at 2.4 A resolution Deposited 2004-06-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–121（121 aa） Chain B 1–121（121 aa）	Not recorded	SO4 SULFATE ION × 1 TDA N-TRIDECANOIC ACID × 2 ACY ACETIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.8；293 K；20mM Sodium acetate, Calcium chloride, 15% PEG8000, 0.2M Ammonium sulphate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.40 Å R-free 0.242
1Y38 Crystal structure of the complex formed between phospholipase A2 dimer and glycerophosphate at 2.4 A resolution Deposited 2004-11-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–121（121 aa） Chain B 1–121（121 aa）	Not recorded	NA SODIUM ION × 1 SO4 SULFATE ION × 1 G3P SN-GLYCEROL-3-PHOSPHATE × 2 PGE TRIETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；25mM Cacodylate, 0.3M ammonium sulphate, 30% PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.44 Å R-free 0.224
1ZR8 Crystal Structure of the complex formed between group II phospholipase A2 and a plant alkaloid ajmaline at 2.0A resolution Deposited 2005-05-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–121（121 aa）	Not recorded	SO4 SULFATE ION × 2 AJM AJMALINE × 1 ACY ACETIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；0.2M AMMONIUM SULPHATE, 30% PEG, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.03 Å R-free 0.221
1ZWP The atomic resolution Crystal structure of the Phospholipase A2 (PLA2) complex with Nimesulide reveals its weaker binding to PLA2 Deposited 2005-06-04	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–121（121 aa）	Not recorded	SO4 SULFATE ION × 4 NIM 4-NITRO-2-PHENOXYMETHANESULFONANILIDE × 1 MOH METHANOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.2M Ammonium sulphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.10 Å R-free 0.147
1ZYX Crystal structure of the complex of a group IIA phospholipase A2 with a synthetic anti-inflammatory agent licofelone at 1.9A resolution Deposited 2005-06-13	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–121（121 aa）	Not recorded	SO4 SULFATE ION × 2 LCF [6-(4-CHLOROPHENYL)-2,2-DIMETHYL-7-PHENYL-2,3-DIHYDRO-1H-PYRROLIZIN-5-YL]ACETIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；Ammonium Sulphate, PEG4000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.95 Å R-free 0.219
2ARM Crystal Structure of the Complex of Phospholipase A2 with a natural compound atropine at 1.2 A resolution Deposited 2005-08-20	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–121（121 aa）	Not recorded	OIN (1R,5S)-8-METHYL-8-AZABICYCLO[3.2.1]OCT-3-YL (2R)-3-HYDROXY-2-PHENYLPROPANOATE × 1 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；ammonium sulphate and PEG 4000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.23 Å R-free 0.204
2B17 Specific binding of non-steroidal anti-inflammatory drugs (NSAIDs) to phospholipase A2: Crystal structure of the complex formed between phospholipase A2 and diclofenac at 2.7 A resolution: Deposited 2005-09-15	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–121（121 aa）	Not recorded	SO4 SULFATE ION × 2 DIF 2-[2,6-DICHLOROPHENYL)AMINO]BENZENEACETIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；ammonium sulphate and PEG 4000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.71 Å R-free 0.211
2DO2 Design of specific inhibitors of phospholipase A2: Crystal structure of the complex formed between a group II Cys 49 phospholipase A2 and a designed pentapeptide Ala-Leu-Ala-Ser-Lys at 2.6A resolution Deposited 2006-04-27	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–121（121 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；298 K；0.2M ammonium sulphate, PEG 4000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.60 Å R-free 0.192
2DPZ Structure of the complex of phospholipase A2 with N-(4-hydroxyphenyl)- acetamide at 2.1 A resolution Deposited 2006-05-18	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–121（121 aa）	Not recorded	SO4 SULFATE ION × 1 TYL N-(4-HYDROXYPHENYL)ACETAMIDE (TYLENOL) × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；298 K；0.2M ammonium sulphate, 30% PEG 4000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.10 Å R-free 0.217
2FNX Design of Specific Peptide Inhibitors of Phospholipase A2 (PLA2): Crystal Structure of the Complex of PLA2 with a Highly Potent Peptide Val-Ile-Ala-Lys at 2.7A Resolution Deposited 2006-01-11	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–121（121 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；298 K；0.2M ammonoium sulfate, 30% PEG4000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.70 Å R-free 0.231
2G58 Crystal structure of a complex of phospholipase A2 with a designed peptide inhibitor Dehydro-Ile-Ala-Arg-Ser at 0.98 A resolution Deposited 2006-02-22	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–121（121 aa）	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；297 K；0.2M AMMONIUM SULPHATE, 50% PEG, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 297K	Resolution 0.98 Å R-free 0.157
2GNS Design of specific peptide inhibitors of phospholipase A2: Crystal structure of the complex formed between a group II phospholipase A2 and a designed pentapeptide Ala- Leu- Val- Tyr- Lys at 2.3 A resolution Deposited 2006-04-11	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–121（121 aa）	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.2；298 K；0.2M ammonium sulphate, 30% PEG 4000, pH 7.2, VAPOR DIFFUSION, temperature 298K	Resolution 2.30 Å R-free 0.212
2O1N Crystal structure of a complex of phospholipase A2 with a peptide Ala-Ile-Ala-Ser at 2.8 A resolution Deposited 2006-11-29	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–121（121 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；PEG 4000, 0.2 M Ammonium Sulphate, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.80 Å R-free 0.227
2OLI Crystal structure of the complex formed between a group II phospholipase A2 and an indole derivative at 2.2 A resolution Deposited 2007-01-19	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–121（121 aa）	Not recorded	IOP INDOLYLPROPIONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；298 K；PEG 4000, Ammonium Sulphate, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.21 Å R-free 0.186
2OTF Crystal structure of the complex formed between phospholipase A2 and atenolol at 1.95 A resolution Deposited 2007-02-08	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–121（121 aa）	Not recorded	2TN 2-(4-(2-HYDROXY-3-(ISOPROPYLAMINO)PROPOXY)PHENYL)ETHANAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；Ammonium Sulphate, PEG 4000, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.95 Å R-free 0.211
2OTH Crystal structure of a ternary complex of phospholipase A2 with indomethacin and nimesulide at 2.9 A resolution Deposited 2007-02-08	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–121（121 aa）	Not recorded	NIM 4-NITRO-2-PHENOXYMETHANESULFONANILIDE × 1 IMN INDOMETHACIN × 1 CCN ACETONITRILE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；298 K；Ammonium Sulphate, PEG4000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.90 Å R-free 0.232
2OUB Crystal structure of the complex formed between phospholipase A2 and atenolol at 2.75 A resolution Deposited 2007-02-10	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–121（121 aa）	Not recorded	2TN 2-(4-(2-HYDROXY-3-(ISOPROPYLAMINO)PROPOXY)PHENYL)ETHANAMIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；298 K；Ammonium sulphate, PEG 4000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.75 Å R-free 0.237
2OYF Crystal Structure of the complex of phospholipase A2 with indole acetic acid at 1.2 A resolution Deposited 2007-02-22	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–121（121 aa）	Not recorded	SO4 SULFATE ION × 5 IAC 1H-INDOL-3-YLACETIC ACID × 1 ACY ACETIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；300 K；0.2M ammonium sulphate, 30% PEG 4000, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 300K	Resolution 1.20 Å R-free 0.208
2PB8 Crystal structure of the complex formed between phospholipase A2 and peptide Ala-Val-Tyr-Ser at 2.0 A resolution Deposited 2007-03-28	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–121（121 aa）	Not recorded	ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；298 K；Acetate, 30% PEG4000, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.218
2PMJ Crystal structure of the complex formed between phospholipase A2 and 1, 2 benzopyrone at 2.4 A resolution Deposited 2007-04-23	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–121（121 aa）	Not recorded	COU COUMARIN × 1 CCN ACETONITRILE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；298 K；0.2M Ammonium sulphate, 30% PEG 4000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.40 Å R-free 0.200
2PVT Crystal structure of a new isoform of phospholipase A2 from russells viper at 2.1 A resolution Deposited 2007-05-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–117（117 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；298 K；0.3M Ammonium sulphate, 30% PEG8000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.10 Å R-free 0.217
2PWS Crystal structure of the complex formed between phospholipase A2 and 2-(4-isobutyl-phenyl)-propionic acid at 2.2 A resolution Deposited 2007-05-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–121（121 aa） Fragment：phospholipase A2	Not recorded	IBP IBUPROFEN × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；298 K；Ammonium Sulphate, PEG 4000, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.21 Å R-free 0.215
2PYC Crystal structure of a monomeric phospholipase A2 from Russell's viper at 1.5A resolution Deposited 2007-05-16	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–121（121 aa）	Not recorded	ACT ACETATE ION × 3 SO4 SULFATE ION × 2 CCN ACETONITRILE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；Sodium acetate, PEG 4000, Acetonitrile, Ammonium sulphate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.50 Å R-free 0.216
2Q1P Crystal Structure of Phospholipase A2 complex with propanol at 1.5 A resolution Deposited 2007-05-25	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–121（121 aa）	Not recorded	SO4 SULFATE ION × 4 POL N-PROPANOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；300 K；0.2M ammonium sulphate, 30% PEG 4000, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 300K	Resolution 1.50 Å R-free 0.205
2QHW Crystal structure of a complex of phospholipase A2 with a gramine derivative at 2.2 resolution Deposited 2007-07-03	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–121（121 aa）	Not recorded	PZZ 3-{3-[(DIMETHYLAMINO)METHYL]-1H-INDOL-7-YL}PROPAN-1-OL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；298 K；Ammoniumu acetate, PEG 4000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.21 Å R-free 0.189
2QU9 Crystal structure of the complex of group II phospholipase A2 with Eugenol Deposited 2007-08-04	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–121（121 aa）	Not recorded	SO4 SULFATE ION × 1 EUG 2-methoxy-4-[(1E)-prop-1-en-1-yl]phenol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；0.2M AMMONIUM SULPHATE, 30% PEG 4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.08 Å R-free 0.217
2QUE Saturation of substrate-binding site using two natural ligands: Crystal structure of a ternary complex of phospholipase A2 with anisic acid and ajmaline at 2.25 A resolution Deposited 2007-08-05	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–121（121 aa）	Not recorded	AJM AJMALINE × 1 ANN 4-METHOXYBENZOIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；298 K；0.2M Ammonium sulphate, 0.2M ammonium acetate, 30% PEG 4000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.25 Å R-free 0.221
2ZBH Crystal structure of the complex of phospholipase A2 with Bavachalcone from Aerva lanata at 2.6 A resolution Deposited 2007-10-20	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–121（121 aa）	Not recorded	BVL (2E)-1-[2-hydroxy-4-methoxy-5-(3-methylbut-2-en-1-yl)phenyl]-3-(4-hydroxyphenyl)prop-2-en-1-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；298 K；50mm Ammonium acetate, 0.2M ammonium sulphate, 30%PEG 4000, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.60 Å R-free 0.227
3CBI Crystal structure of the ternary complex of phospholipase A2 with ajmaline and anisic acid at 3.1 A resolution Deposited 2008-02-22	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–121（121 aa）	Not recorded	AJM AJMALINE × 1 ANN 4-METHOXYBENZOIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；0.2M AMMONIUM SULPHATE, 30% PEG-4K, 0.1M SODIUM ACETATE BUFFER, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.15 Å R-free 0.250
3CBI Crystal structure of the ternary complex of phospholipase A2 with ajmaline and anisic acid at 3.1 A resolution Deposited 2008-02-22	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–121（121 aa）	Not recorded	AJM AJMALINE × 1 ANN 4-METHOXYBENZOIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；0.2M AMMONIUM SULPHATE, 30% PEG-4K, 0.1M SODIUM ACETATE BUFFER, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.15 Å R-free 0.250
3CBI Crystal structure of the ternary complex of phospholipase A2 with ajmaline and anisic acid at 3.1 A resolution Deposited 2008-02-22	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–121（121 aa）	Not recorded	AJM AJMALINE × 1 ANN 4-METHOXYBENZOIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；0.2M AMMONIUM SULPHATE, 30% PEG-4K, 0.1M SODIUM ACETATE BUFFER, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.15 Å R-free 0.250
3CBI Crystal structure of the ternary complex of phospholipase A2 with ajmaline and anisic acid at 3.1 A resolution Deposited 2008-02-22	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–121（121 aa）	Not recorded	AJM AJMALINE × 1 ANN 4-METHOXYBENZOIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；0.2M AMMONIUM SULPHATE, 30% PEG-4K, 0.1M SODIUM ACETATE BUFFER, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.15 Å R-free 0.250
3G8F Crystal structure of the complex formed between a group II phospholipase A2 and designed peptide inhibitor carbobenzoxy-dehydro-val-ala-arg-ser at 1.2 A resolution Deposited 2009-02-12	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–121（121 aa）	Not recorded	SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.2M AMMONIUM SULPHATE, 30% PEG, CaCl2, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.25 Å R-free 0.210
3H1X Simultaneous inhibition of anti-coagulation and inflammation: Crystal structure of phospholipase A2 complexed with indomethacin at 1.4 A resolution reveals the presence of the new common ligand binding site Deposited 2009-04-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–121（121 aa）	Not recorded	IMN INDOMETHACIN × 1 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；0.3M AMMONIUM SULPHATE, 30% PEG 4000 , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.40 Å R-free 0.207

52 other PDB entries and 66 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PA28_DABRP
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–121； UniProt 1–121

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

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	2qvd
Deposition date deposition_date	2007-08-08
Structure title title	Identification of a potent anti-inflammatory agent from the natural extract of plant Cardiospermun helicacabum: Crystal structure of the complex of phospholipase A2 with Benzo(g)-1,3-benzodioxolo(5,6-a)quinolizinium, 5,6-dihydro-9,10-dimethoxy at 1.93 A resolution
Keywords keywords	;phospholipids, membrane, hydrolysis, inhibitor, plant extraxt, Lipid degradation, Metal-binding, Neurotoxin, Presynaptic neurotoxin, Secreted, Toxin, HYDROLASE-HYDROLASE INHIBITOR complex ;; HYDROLASE/HYDROLASE INHIBITOR
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	15.13 Å
Radius of gyration Rg (electron density) rg_electron	14.39 Å
Forward intensity I(0) i0	4091130.00
Molecular weight molecular_weight	13934.0 kDa
Excluded volume excluded_volume	17246 Å³
Envelope volume envelope_volume	19710 Å³
Hydration-shell volume shell_volume	11835 Å³
Envelope diameter envelope_diameter	51.7 Å
Shell Rg shell_rg	19.81 Å
Envelope Rg envelope_rg	14.81 Å
Shape Rg shape_rg	14.36 Å
Total Rg total_rg	15.58 Å
Total atoms total_atoms	968
Residues n_residues	121
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

▼

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

Maximum dimension Dmax dmax	52.6 Å
Rg (real space) rg_real	15.08 Å
Rg uncertainty (real space) rg_real_error	0.32 Å
I(0) (real space) i0_real	4.0910e+06
I(0) uncertainty (real space) i0_real_error	4.5880e+04
Rg (reciprocal space) rg_reciprocal	15.08 Å
I(0) (reciprocal space) i0_reciprocal	4091000.0000
Solution quality estimate total_estimate	0.8645
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	16.6 Å
Skewness Skewness skewness	0.260
Kurtosis Kurtosis kurtosis	-0.354
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1203000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.764; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.953; Smooth: 0.989

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (3)

▼

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2qvda_
Class class	a — All alpha proteins
Fold Fold fold	a.133 — Phospholipase A2, PLA2
Superfamily Superfamily superfamily	a.133.1 — Phospholipase A2, PLA2
Family Family family	a.133.1.2 — Vertebrate phospholipase A2

CATH v4.4 (1 domains)

Domain ID domain_id	2qvdA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	90 — Phospholipase A2
Homologous superfamily homologous superfamily	10 — Phospholipase A2 domain

▶

8. Citations (1)

▶

Unit-cell length a length_a	53.311 Å
Unit-cell length b length_b	53.311 Å
Unit-cell length c length_c	48.379 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	4

Space group space_group	P 43
Space-group number int_tables_number	78
Crystal system crystal_system	—

Resolution resolution	1.930 Å
Low-resolution limit resolution_low	53.450 Å
R factor r_factor	0.1777
R_work r_work	0.1754
R_free r_free	0.2243

Description description	Phospholipase A2 VRV-PL-VIIIa
Molecular weight formula_weight	13629.8 kDa
EC 编号 ec_number	3.1.1.4
Source method src_method	nat
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1080

Identification of a potent anti-inflammatory agent from the natural extract of plant Cardiospermun helicacabum: Crystal structure of the complex of phospholipase A2 with Benzo(g)-1,3-benzodioxolo(5,6-a)quinolizinium, 5,6-dihydro-9,10-dimethoxy at 1.93 A resolution

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

Phospholipase A2 VRV-PL-VIIIa

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	BERBERINE
Molecular weight formula_weight	336.4 kDa
Source method src_method	syn
Copy count entity_count	1

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	112

fit	/app/data/saxs_computation/qv/2qvd/2qvd.fit
pddf	/app/data/pr_computation/qv/2qvd/2qvd.pr.out
profile	/app/data/saxs_computation/qv/2qvd/2qvd.dat