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2zp5

Carboxylic ester hydrolase, single mutant d49k of bovine pancreatic pla2 enzyme

Method: X-RAY DIFFRACTION Dmax: 51.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Phospholipase A2

Bos taurus

UniProt P00593

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 23–145 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

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 2ZP5 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 mutation/modification 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 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 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 mutation/modification 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 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 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 23–145（123 aa）
Not recorded CA CALCIUM ION × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.90 Å
1FDK CARBOXYLIC ESTER HYDROLASE (PLA2-MJ33 INHIBITOR COMPLEX) Deposited 1997-09-04 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 23–145（123 aa）
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
1G4I Crystal structure of the bovine pancreatic phospholipase A2 at 0.97A Deposited 2000-10-27 Different mutation/modification 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 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 oligomeric state 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 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 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 oligomeric state 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 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 oligomeric state 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 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 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 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 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 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 mutation/modification 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 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 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 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 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 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 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 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 mutation/modification 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 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 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 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 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
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 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 mutation/modification 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

SAXS profile for 2zp5

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2zp5
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2zp5
Deposition date deposition_date2008-06-27
Structure title titleCarboxylic ester hydrolase, single mutant d49k of bovine pancreatic pla2 enzyme
Keywords keywords;HYDROLASE, ACTIVE SITE MUTANT, METAL BINDING PROTEIN, Calcium, Lipid degradation, Metal-binding, Pyrrolidone carboxylic acid, Secreted ;; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier15.46 Å
Radius of gyration Rg (electron density) rg_electron14.46 Å
Forward intensity I(0) i04455810.00
Molecular weight molecular_weight13885.0 kDa
Excluded volume excluded_volume16864 ų
Envelope volume envelope_volume19437 ų
Hydration-shell volume shell_volume11695 ų
Envelope diameter envelope_diameter52.9 Å
Shell Rg shell_rg19.84 Å
Envelope Rg envelope_rg14.86 Å
Shape Rg shape_rg14.43 Å
Total Rg total_rg15.57 Å
Total atoms total_atoms960
Residues n_residues123
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax51.7 Å
Rg (real space) rg_real15.42 Å
Rg uncertainty (real space) rg_real_error0.40 Å
I(0) (real space) i0_real4.4560e+06
I(0) uncertainty (real space) i0_real_error5.4410e+04
Rg (reciprocal space) rg_reciprocal15.42 Å
I(0) (reciprocal space) i0_reciprocal4456000.0000
Solution quality estimate total_estimate0.8081
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary17.7 Å
Skewness Skewness skewness0.261
Kurtosis Kurtosis kurtosis-0.375
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha872400.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.842; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd2zp5a_
Class classa — All alpha proteins
Fold Fold folda.133 — Phospholipase A2, PLA2
Superfamily Superfamily superfamilya.133.1 — Phospholipase A2, PLA2
Family Family familya.133.1.2 — Vertebrate phospholipase A2

CATH v4.4 (1 domains)

Domain ID domain_id2zp5A00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology90 — Phospholipase A2
Homologous superfamily homologous superfamily10 — Phospholipase A2 domain
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8. Citations (1)

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9. Files and Curves (10)