1fdk

CARBOXYLIC ESTER HYDROLASE (PLA2-MJ33 INHIBITOR COMPLEX)

Method: X-RAY DIFFRACTION D_max: 50.5 Å Quality: REASONABLE

▼

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

PHOSPHOLIPASE A2

Bos taurus

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 23–145	Not recorded	CA CALCIUM ION × 2 GLE 1-DECYL-3-TRIFLUORO ETHYL-SN-GLYCERO-2-PHOSPHOMETHANOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.2；CRYSTALS WERE GROWN BY CO-CRYSTALLIZATION BY THE HANGING DROP VAPOR DIFFUSION METHOD USING THE CONDITIONS 5 (MICRO)L OF THE MUTANT PROTEIN (15 MG/ML OF THE PROTEIN), 5MM CACL2, 50MM TRIS BUFFER, PH 7.2, 2.0 (MICRO)L OF 75% MPD IN THE DROPLET AND 1(MICRO)L OF MJ33 INHIBITOR SOLUTION (2.5MM CONCENTRATION). THE RESERVOIR CONTAINED (50%) OF MPD., vapor diffusion - hanging drop	Resolution 1.91 Å R-free 0.280

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 1FDK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BP2 STRUCTURE OF BOVINE PANCREATIC PHOSPHOLIPASE A2 AT 1.7 ANGSTROMS RESOLUTION Deposited 1981-04-06	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 23–145（123 aa）	Not recorded	CA CALCIUM ION × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.70 Å
1BPQ PHOSPHOLIPASE A2 ENGINEERING. X-RAY STRUCTURAL AND FUNCTIONAL EVIDENCE FOR THE INTERACTION OF LYSINE-56 WITH SUBSTRATES Deposited 1991-10-28	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 23–145（123 aa）	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å
1BVM SOLUTION NMR STRUCTURE OF BOVINE PANCREATIC PHOSPHOLIPASE A2, 20 STRUCTURES Deposited 1998-09-14	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 23–145（123 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；310 K；Ionic strength (raw mmCIF value) 300 mM NACL, 50 mM CACL2 NMR sample composition H2O AND D2O, 50 MM CACL2, 300 MM NACL	Resolution not provided
1C74 Structure of the double mutant (K53,56M) of phospholipase A2 Deposited 2000-01-22	Different mutation/modification 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 23–145（123 aa）	Mutation：K53M, K56M	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions vapor diffusion method；pH 7.2；293 K；Tris Buffer, MPD, 50% MPD reservoir, 15Mg/ml protein, 5 mM CaCl2, pH 7.2, vapor diffusion method, temperature 293.0K	Resolution 1.90 Å R-free 0.224
1CEH STRUCTURE AND FUNCTION OF THE CATALYTIC SITE MUTANT ASP99ASN OF PHOSPHOLIPASE A2: ABSENCE OF CONSERVED STRUCTURAL WATER Deposited 1994-11-16	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 23–145（123 aa）	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å
1G4I Crystal structure of the bovine pancreatic phospholipase A2 at 0.97A Deposited 2000-10-27	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 23–145（123 aa）	Not recorded	CA CALCIUM ION × 1 CL CHLORIDE ION × 1 MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 3 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions SMALL TUBES；pH 7.6；293 K；MPD, calcium chloride, Tris buffer, pH 7.6, SMALL TUBES, temperature 293K	Resolution 0.97 Å
1GH4 Structure of the triple mutant (K56M, K120M, K121M) of phospholipase A2 Deposited 2000-11-09	Different mutation/modification 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 23–145（123 aa）	Mutation：K56M,K120M,K121M	CA CALCIUM ION × 2 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions vapor diffusion method；pH 7.2；293 K；Tris Buffer, MPD, 70% MPD reservoir, 17-20Mg/ml protein, 5 mM CaCl2, pH 7.2, vapor diffusion method, temperature 293.0K	Resolution 1.90 Å R-free 0.259
1IRB CARBOXYLIC ESTER HYDROLASE Deposited 1997-08-13	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 23–145（123 aa）	Mutation：K120A, K121A	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；CRYSTALS WERE GROWN BY THE HANGING DROP VAPOR DIFFUSION METHOD USING THE CONDITIONS DESCRIBED FOR THE WILD TYPE ENZYME (NOEL ET AL., 1991), pH 7.2, vapor diffusion - hanging drop	Resolution 1.90 Å
1KVW CARBOXYLIC ESTER HYDROLASE, SINGLE MUTANT H48Q OF BOVINE PANCREATIC PLA2 ENZYME Deposited 1998-04-24	Different mutation/modification 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 23–145（123 aa）	Mutation：H48Q	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.2；CRYSTALS WERE GROWN BY THE VAPOR DIFFUSION METHOD USING THE CONDITIONS 5 (MICRO)L OF THE MUTANT PROTEIN (15MG/ML OF THE PROTEIN), 5MM CACL2, 50MM TRIS BUFFER, PH 7.2 AND 2 (MICRO)L OF 40% MPD AND (60%) OF MPD IN THE RESERVOIR, vapor diffusion	Resolution 1.95 Å R-free 0.314
1KVX CARBOXYLIC ESTER HYDROLASE, SINGLE MUTANT D99A OF BOVINE PANCREATIC PLA2, 1.9 A ORTHORHOMBIC FORM Deposited 1998-04-28	Different mutation/modification 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 23–145（123 aa）	Mutation：D99A	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；CRYSTALS WERE GROWN BY CO-CRYSTALLIZATION BY THE HANGING DROP VAPOR DIFFUSION METHOD USING THE CONDITIONS 5 (MICRO)L OF THE PROTEIN (15 MG/ML OF THE PROTEIN), 5MM CACL2, 50MM TRIS BUFFER, PH 7.2 AND 2.0 (MICRO)L OF 50% MPD IN THE DROPLET. THE RESERVOIR CONTAINED (75%) OF MPD., vapor diffusion - hanging drop	Resolution 1.90 Å R-free 0.313
1KVY CARBOXYLIC ESTER HYDROLASE, SINGLE MUTANT D49E COORDINATED TO CALCIUM Deposited 1998-04-29	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 23–145（123 aa）	Mutation：D49E	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；CRYSTALS WERE GROWN OVER A PERIOD OF ELEVEN MONTHS USING THE HANGING DROP VAPOR DIFFUSION METHOD BY EMPLOYING THE CONDITIONS 5 (MICRO)L OF THE PROTEIN (20 MG/ML OF THE PROTEIN), 5MM CACL2, 50MM TRIS BUFFER, PH 7.2 AND 2.5 (MICRO)L OF 75% MPD IN THE DROPLET. THE RESERVOIR CONTAINED (55%) OF MPD., vapor diffusion - hanging drop	Resolution 1.90 Å R-free 0.277
1MKS CARBOXYLIC ESTER HYDROLASE, TRIGONAL FORM OF THE TRIPLE MUTANT Deposited 1997-08-27	Different mutation/modification 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 23–145（123 aa）	Mutation：Y52F, Y73F, D99N	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；CRYSTALS WERE GROWN BY THE HANGING DROP VAPOR DIFFUSION METHOD FROM DROPLETS CONTAINING 5 (MICRO)L OF THE MUTANT PROTEIN (15MG/ML) 5MM CACL2, 50MM TRIS BUFFER, PH 7.2 AND 2 (MICRO)L OF 75% MPD AND (50%) OF MPD IN THE RESERVOIR, vapor diffusion - hanging drop	Resolution 1.90 Å
1MKT CARBOXYLIC ESTER HYDROLASE, 1.72 ANGSTROM TRIGONAL FORM OF THE BOVINE RECOMBINANT PLA2 ENZYME Deposited 1997-09-06	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 23–145（123 aa）	Mutation：K122N	CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.2；CRYSTALS WERE GROWN BY THE VAPOR DIFFUSION METHOD USING THE CONDITIONS 5 (MICRO)L OF THE MUTANT PROTEIN (15MG/ML OF THE PROTEIN), 5MM CACL2, 50MM TRIS BUFFER, PH 7.2 AND 2 (MICRO)L OF 75% MPD AND (50%) OF MPD IN THE RESERVOIR, vapor diffusion	Resolution 1.72 Å R-free 0.284
1MKU CARBOXYLIC ESTER HYDROLASE, ORTHORHOMBIC FORM OF THE TRIPLE MUTANT Deposited 1997-09-10	Different mutation/modification 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 23–145（123 aa）	Mutation：Y52F, Y73F, D99N	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；CRYSTALS WERE GROWN BY THE HANGING DROP VAPOR DIFFUSION METHOD, pH 7.2, vapor diffusion - hanging drop	Resolution 1.80 Å
1MKV CARBOXYLIC ESTER HYDROLASE COMPLEX (PLA2 + TRANSITION STATE ANALOG COMPLEX) Deposited 1997-09-13	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 23–145（123 aa）	Not recorded	CA CALCIUM ION × 2 GEL 1-O-OCTYL-2-HEPTYLPHOSPHONYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；CRYSTALS WERE GROWN BY CO-CRYSTALLIZATION BY THE HANGING DROP VAPOR DIFFUSION METHOD USING THE CONDITIONS 5 (MICRO)L OF THE MUTANT PROTEIN (20MG/ML OF THE PROTEIN), 5MM CACL2, 50MM TRIS BUFFER, PH 7.2 AND 2.5 (MICRO)L OF 75% MPD AND 2.0 (MICRO)L OF (2MM) IN THE DROPLET. THE RESERVOIR CONTAINED (50%) OF MPD., pH 7.5, vapor diffusion - hanging drop	Resolution 1.89 Å
1O2E Structure of the triple mutant (K53,56,120M) + Anisic acid complex of phospholipase A2 Deposited 2003-03-05	Different mutation/modification 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 23–145（123 aa）	Mutation：K53M, K56M and K120M (triple mutant)	CA CALCIUM ION × 1 ANN 4-METHOXYBENZOIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions vapor diffusion method；pH 7.2；293 K；50 mM Tris Buffer, MPD,70% MPD reservoir,17-20Mg/ml prot,5 mM CaCl2, 1 microlitre of anisic acid, pH 7.2, vapor diffusion method, temperature 293.0K	Resolution 2.60 Å R-free 0.241
1O3W Structure of the inhibitor free triple mutant (K53,56,120M) of phospholipase A2 Deposited 2003-04-14	Different mutation/modification 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 23–145（123 aa）	Mutation：K53M, K56M, K120M	CA CALCIUM ION × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions vapor diffusion method；pH 7.2；293 K；50 mM Tris Buffer, 70% MPD reservoir,17-20Mg/ml prot,5 mM CaCl2 and 60% MPD in the droplet, pH 7.2, vapor diffusion method, temperature 293.0K	Resolution 1.85 Å R-free 0.232
1UNE CARBOXYLIC ESTER HYDROLASE, 1.5 ANGSTROM ORTHORHOMBIC FORM OF THE BOVINE RECOMBINANT PLA2 Deposited 1997-11-05	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 23–145（123 aa）	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；CRYSTALS WERE GROWN BY CO-CRYSTALLIZATION BY THE HANGING DROP VAPOR DIFFUSION METHOD USING THE CONDITIONS 5 (MICRO)L OF THE PROTEIN (15 MG/ML OF THE PROTEIN), 5MM CACL2, 50MM TRIS BUFFER, PH 7.2 AND 3.0 (MICRO)L OF 50% MPD IN THE DROPLET. THE RESERVOIR CONTAINED (50%) OF MPD., vapor diffusion - hanging drop	Resolution 1.50 Å R-free 0.228
1VKQ A re-determination of the structure of the triple mutant (K53,56,120M) of phospholipase A2 at 1.6A resolution using sulphur-SAS at 1.54A wavelength Deposited 2004-06-12	Different mutation/modification 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 23–145（123 aa）	Mutation：K53M, K56M, K120M	CA CALCIUM ION × 1 CL CHLORIDE ION × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions vapor diffusion method；pH 7.2；293 K；50 mM Tris Buffer, 70% MPD reservoir,17-20Mg/ml prot,5 mM CaCl2 and 60% MPD in the droplet, pH 7.2, vapor diffusion method, temperature 293.0K	Resolution 1.60 Å R-free 0.217
1VL9 Atomic resolution (0.97A) structure of the triple mutant (K53,56,121M) of bovine pancreatic phospholipase A2 Deposited 2004-07-15	Different mutation/modification 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 23–145（123 aa）	Mutation：K53M, K56M, K121M	CA CALCIUM ION × 2 CL CHLORIDE ION × 1 MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 3 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.2；293 K；50 mM Tris Buffer, 70% MPD reservoir,17-20Mg/ml prot,5 mM CaCl2 and 60% MPD in the droplet, pH 7.2, temperature 293.0K, VAPOR DIFFUSION	Resolution 0.97 Å R-free 0.134
2B96 Third Calcium ion found in an inhibitor bound phospholipase A2 Deposited 2005-10-11	Different mutation/modification 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 23–145（123 aa）	Mutation：K53M, K56M, K121M	CA CALCIUM ION × 3 CL CHLORIDE ION × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 4 ANN 4-METHOXYBENZOIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；50 mM Tris Buffer, 70% MPD reservoir, 15-20 mg/ml protein, 5mM CaCl2, 1microlitre anisic acid, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.70 Å R-free 0.221
2BAX Atomic Resolution Structure of the Double Mutant (K53,56M) of Bovine Pancreatic Phospholipase A2 Deposited 2005-10-15	Different mutation/modification 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 23–145（123 aa）	Mutation：K53M, K56M	CA CALCIUM ION × 1 CL CHLORIDE ION × 1 MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 4 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.2；293 K；The double mutant protein was dissolved in 50 mM Tris buffer (7.2) containing 5mM of CaCl2, to a final protein Concentration of 17-20 mg/ml. The crystallization droplet contained 5 micro litre of protein and 2 micro litre of 60% MPD and the reservior contianined 1000 micro litre of 70% MPD, VAPOR DIFFUSION, temperature 293K	Resolution 1.10 Å R-free 0.156
2BCH A possible of Second calcium ion in interfacial binding: Atomic and Medium resolution crystal structures of the quadruple mutant of phospholipase A2 Deposited 2005-10-19	Different mutation/modification 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 23–145（123 aa）	Mutation：K53M, K56M, K120M, K121M	CA CALCIUM ION × 1 CL CHLORIDE ION × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.2；293 K；The crystallization droplet contained 5 micro litre of protein and 2 mirco litre of MPD (50%) and a reservoir contained 50% of MPD., pH 7.2, VAPOR DIFFUSION, temperature 293K	Resolution 1.10 Å R-free 0.133
2BD1 A possible role of the second calcium ion in interfacial binding: Atomic and medium resolution crystal structures of the quadruple mutant of phospholipase A2 Deposited 2005-10-19	Different mutation/modification 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 23–145（123 aa）	Mutation：K53M, K56M, K120M, K121M	CA CALCIUM ION × 2 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.2；293 K；The crystallization droplet contained 5 micro litre of protein (18 to 20 mg/ml) in 50 mM tris buffer with 2 micro litre of MPD (60%) and the reservoir contained 70% of MPD., pH 7.2, VAPOR DIFFUSION, temperature 293K	Resolution 1.90 Å R-free 0.240
2BD1 A possible role of the second calcium ion in interfacial binding: Atomic and medium resolution crystal structures of the quadruple mutant of phospholipase A2 Deposited 2005-10-19	Different mutation/modification 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 23–145（123 aa）	Mutation：K53M, K56M, K120M, K121M	CA CALCIUM ION × 2 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.2；293 K；The crystallization droplet contained 5 micro litre of protein (18 to 20 mg/ml) in 50 mM tris buffer with 2 micro litre of MPD (60%) and the reservoir contained 70% of MPD., pH 7.2, VAPOR DIFFUSION, temperature 293K	Resolution 1.90 Å R-free 0.240
2BP2 THE STRUCTURE OF BOVINE PANCREATIC PROPHOSPHOLIPASE A2 AT 3.0 ANGSTROMS RESOLUTION Deposited 1981-06-05	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 16–145（130 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.00 Å
2BPP PHOSPHOLIPASE A2 ENGINEERING. X-RAY STRUCTURAL AND FUNCTIONAL EVIDENCE FOR THE INTERACTION OF LYSINE-56 WITH SUBSTRATES Deposited 1992-01-17	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 23–145（123 aa）	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.80 Å
2ZP3 Carboxylic ester hydrolase, single mutant d49n of bovine pancreatic pla2 enzyme Deposited 2008-06-27	Different mutation/modification 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 23–145（123 aa）	Mutation：D49N	CA CALCIUM ION × 1 CL CHLORIDE ION × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；5mm CACL2, 50mm tris buffer, 70% MPD, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.238
2ZP4 Carboxylic ester hydrolase, single mutant h48n of bovine pancreatic pla2 enzyme Deposited 2008-06-27	Different mutation/modification 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 23–145（123 aa）	Mutation：H48N	CA CALCIUM ION × 2 CL CHLORIDE ION × 1 MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；5mm CACL2, 50mm tris buffer, pH 7.2, 60% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.201
2ZP5 Carboxylic ester hydrolase, single mutant d49k of bovine pancreatic pla2 enzyme Deposited 2008-06-27	Different mutation/modification 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 23–145（123 aa）	Mutation：D49K	CA CALCIUM ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；5mm CACL2, 50mm tris buffer, PH 7.2, 60% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.235
3BP2 ROLE OF THE N-TERMINUS IN THE INTERACTION OF PANCREATIC PHOSPHOLIPASE A2 WITH AGGREGATED SUBSTRATES. PROPERTIES AND CRYSTAL STRUCTURE OF TRANSAMINATED PHOSPHOLIPASE A2 Deposited 1983-06-27	Different construct Different mutation/modification 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 24–145（122 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å
4BP2 CRYSTALLOGRAPHIC REFINEMENT OF BOVINE PRO-PHOSPHOLIPASE A2 AT 1.6 ANGSTROMS RESOLUTION Deposited 1990-09-07	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 16–145（130 aa）	Not recorded	CA CALCIUM ION × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.60 Å

31 other PDB entries and 32 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PA21B_BOVIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–123； UniProt 23–145

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	1fdk
Deposition date deposition_date	1997-09-04
Structure title title	CARBOXYLIC ESTER HYDROLASE (PLA2-MJ33 INHIBITOR COMPLEX)
Keywords keywords	LIPID DEGRADATION, ENZYME, CARBOXYLIC ESTER HYDROLASE, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	15.20 Å
Radius of gyration Rg (electron density) rg_electron	14.23 Å
Forward intensity I(0) i0	4623080.00
Molecular weight molecular_weight	14243.0 kDa
Excluded volume excluded_volume	17306 Å³
Envelope volume envelope_volume	19448 Å³
Hydration-shell volume shell_volume	11794 Å³
Envelope diameter envelope_diameter	50.0 Å
Shell Rg shell_rg	19.73 Å
Envelope Rg envelope_rg	14.68 Å
Shape Rg shape_rg	14.24 Å
Total Rg total_rg	15.27 Å
Total atoms total_atoms	984
Residues n_residues	123
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	50.5 Å
Rg (real space) rg_real	15.16 Å
Rg uncertainty (real space) rg_real_error	0.26 Å
I(0) (real space) i0_real	4.6230e+06
I(0) uncertainty (real space) i0_real_error	5.4540e+04
Rg (reciprocal space) rg_reciprocal	15.17 Å
I(0) (reciprocal space) i0_reciprocal	4623000.0000
Solution quality estimate total_estimate	0.7407
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	16.6 Å
Skewness Skewness skewness	0.284
Kurtosis Kurtosis kurtosis	-0.375
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1090000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.849; Stabil: 1.000; Sysdev: 0.368; Positv: 1.000; Valcen: 0.981; Smooth: 0.993

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	PHOSPHOLIPASE A2
Molecular weight formula_weight	13810.5 kDa
EC 编号 ec_number	3.1.1.4
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1070

ALWQFNGMIKCKIPSSEPLLDFNNYGCYCGLGGSGTPVDDLDRCCQTHDNCYKQAKKLDSCKVLVDNPYTNNYSYSCSNNEITCSSENNACEAFICNCDRNAAICFSKVPYNKEHKNLDKKNC

来源 Source

来源生物 organism	Bos taurus
通用名 common_name	cattle
NCBI Class编号 ncbi_taxonomy_id	9913
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	1-DECYL-3-TRIFLUORO ETHYL-SN-GLYCERO-2-PHOSPHOMETHANOL
Molecular weight formula_weight	408.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	86

▼

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1fdka_
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	1fdkA00
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 (6)

▶

Unit-cell length a length_a	46.360 Å
Unit-cell length b length_b	46.360 Å
Unit-cell length c length_c	102.560 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	6

Space group space_group	P 31 2 1
Space-group number int_tables_number	152
Crystal system crystal_system	—

Resolution resolution	1.910 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1840
R_work r_work	0.1840
R_free r_free	0.2800

fit	/app/data/saxs_computation/fd/1fdk/1fdk.fit
pddf	/app/data/pr_computation/fd/1fdk/1fdk.pr.out
profile	/app/data/saxs_computation/fd/1fdk/1fdk.dat