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1pod

STRUCTURES OF FREE AND INHIBITED HUMAN SECRETORY PHOSPHOLIPASE A2 FROM INFLAMMATORY EXUDATE

Method: X-RAY DIFFRACTION Dmax: 49.6 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PHOSPHOLIPASE A2

Homo sapiens

UniProt P14555

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 21–144 Not recorded CA CALCIUM ION × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 2.10 Å

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 1POD Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1AYP A PROBE MOLECULE COMPOSED OF SEVENTEEN PERCENT OF TOTAL DIFFRACTING MATTER GIVES CORRECT SOLUTIONS IN MOLECULAR REPLACEMENT Deposited 1994-07-19 Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 21–144（124 aa）
Chain F 21–144（124 aa）
Not recorded CA CALCIUM ION × 4 INB 1-OCTADECYL-2-ACETAMIDO-2-DEOXY-SN-GLYCEROL-3-PHOSPHOETHYLMETHYL SULFIDE × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.57 Å
1AYP A PROBE MOLECULE COMPOSED OF SEVENTEEN PERCENT OF TOTAL DIFFRACTING MATTER GIVES CORRECT SOLUTIONS IN MOLECULAR REPLACEMENT Deposited 1994-07-19 Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain B 21–144（124 aa）
Chain E 21–144（124 aa）
Not recorded CA CALCIUM ION × 4 INB 1-OCTADECYL-2-ACETAMIDO-2-DEOXY-SN-GLYCEROL-3-PHOSPHOETHYLMETHYL SULFIDE × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.57 Å
1AYP A PROBE MOLECULE COMPOSED OF SEVENTEEN PERCENT OF TOTAL DIFFRACTING MATTER GIVES CORRECT SOLUTIONS IN MOLECULAR REPLACEMENT Deposited 1994-07-19 Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 21–144（124 aa）
Chain D 21–144（124 aa）
Not recorded CA CALCIUM ION × 4 INB 1-OCTADECYL-2-ACETAMIDO-2-DEOXY-SN-GLYCEROL-3-PHOSPHOETHYLMETHYL SULFIDE × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.57 Å
1BBC STRUCTURE OF RECOMBINANT HUMAN RHEUMATOID ARTHRITIC SYNOVIAL FLUID PHOSPHOLIPASE A2 AT 2.2 ANGSTROMS RESOLUTION Deposited 1992-05-04 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 21–144（124 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.20 Å
1DB4 HUMAN S-PLA2 IN COMPLEX WITH INDOLE 8 Deposited 1999-11-02 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 21–144（124 aa）
Not recorded CA CALCIUM ION × 2 8IN [3-(1-BENZYL-3-CARBAMOYLMETHYL-2-METHYL-1H-INDOL-5-YLOXY)-PROPYL-]-PHOSPHONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；297 K；10 MG/ML OF PROTEIN; 50 MM BUFFER (MES OR MOPS), 1% PYRIDINE, pH 7.0, VAPOR DIFFUSION, temperature 297K
Resolution 2.20 Å R-free 0.256
1DB5 HUMAN S-PLA2 IN COMPLEX WITH INDOLE 6 Deposited 1999-11-02 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 21–144（124 aa）
Not recorded CA CALCIUM ION × 2 6IN 4-(1-BENZYL-3-CARBAMOYLMETHYL-2-METHYL-1H-INDOL-5-YLOXY)-BUTYRIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；297 K；10 mg/ml of protein; 50 mM buffer (MES or MOPS), 1% pyridine., pH 7.0, VAPOR DIFFUSION, temperature 297K
Resolution 2.80 Å R-free 0.240
1DCY CRYSTAL STRUCTURE OF HUMAN S-PLA2 IN COMPLEX WITH INDOLE 3 ACTIVE SITE INHIBITOR Deposited 1999-11-05 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 21–144（124 aa）
Not recorded CA CALCIUM ION × 2 I3N 1-BENZYL-5-METHOXY-2-METHYL-1H-INDOL-3-YL)-ACETIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7；297 K；10 MG/ML OF PROTEIN, 50 MM BUFFER (MES OF MOPS), 1% PYRIDINE, AN INHIBITOR CONCENTRATION OF 1.5 MOLAR EQUIVALENT, pH 7.0, VAPOR DIFFUSION, temperature 297K
Resolution 2.70 Å R-free 0.269
1J1A PANCREATIC SECRETORY PHOSPHOLIPASE A2 (IIa) WITH ANTI-INFLAMMATORY ACTIVITY Deposited 2002-12-03 Different construct 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 21–144（124 aa）
Chain B 21–144（124 aa）
Not recorded CA CALCIUM ION × 4 BHP (S)-5-(4-BENZYLOXY-PHENYL)-4-(7-PHENYL-HEPTANOYLAMINO)-PENTANOIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Sodium Chloride, Calcium Chloride, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.20 Å R-free 0.258
1KQU Human phospholipase A2 complexed with a substrate anologue Deposited 2002-01-07 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 21–144（124 aa）
Not recorded CA CALCIUM ION × 2 BR4 6-PHENYL-4(R)-(7-PHENYL-HEPTANOYLAMINO)-HEXANOIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；293 K；sodium Chloride, Calcium Chloride, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Resolution 2.10 Å R-free 0.240
1KVO HUMAN PHOSPHOLIPASE A2 COMPLEXED WITH A HIGHLY POTENT SUBSTRATE ANOLOGUE Deposited 1996-07-29 Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 21–144（124 aa）
Chain B 21–144（124 aa）
Not recorded CA CALCIUM ION × 4 OAP 4-(S)-[(1-OXO-7-PHENYLHEPTYL)AMINO]-5-[4-(PHENYLMETHYL)PHENYLTHIO]PENTANOIC ACID × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å R-free 0.273
1KVO HUMAN PHOSPHOLIPASE A2 COMPLEXED WITH A HIGHLY POTENT SUBSTRATE ANOLOGUE Deposited 1996-07-29 Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 21–144（124 aa）
Chain D 21–144（124 aa）
Not recorded CA CALCIUM ION × 4 OAP 4-(S)-[(1-OXO-7-PHENYLHEPTYL)AMINO]-5-[4-(PHENYLMETHYL)PHENYLTHIO]PENTANOIC ACID × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å R-free 0.273
1KVO HUMAN PHOSPHOLIPASE A2 COMPLEXED WITH A HIGHLY POTENT SUBSTRATE ANOLOGUE Deposited 1996-07-29 Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain E 21–144（124 aa）
Chain F 21–144（124 aa）
Not recorded CA CALCIUM ION × 4 OAP 4-(S)-[(1-OXO-7-PHENYLHEPTYL)AMINO]-5-[4-(PHENYLMETHYL)PHENYLTHIO]PENTANOIC ACID × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.00 Å R-free 0.273
1N28 Crystal structure of the H48Q mutant of human group IIA phospholipase A2 Deposited 2002-10-22 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 21–144（124 aa）
Mutation：N1A, H48Q CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；277 K；NaCl, CaCl2, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.50 Å R-free 0.207
1N28 Crystal structure of the H48Q mutant of human group IIA phospholipase A2 Deposited 2002-10-22 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 21–144（124 aa）
Mutation：N1A, H48Q CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；277 K；NaCl, CaCl2, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.50 Å R-free 0.207
1N29 Crystal structure of the N1A mutant of human group IIA phospholipase A2 Deposited 2002-10-22 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 21–144（124 aa）
Mutation：N1A CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；NaCl, CaCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.60 Å R-free 0.320
1POE STRUCTURES OF FREE AND INHIBITED HUMAN SECRETORY PHOSPHOLIPASE A2 FROM INFLAMMATORY EXUDATE Deposited 1992-09-07 Different construct Different mutation/modification Different ligand/ion Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 21–144（124 aa）
Chain B 21–144（124 aa）
Not recorded CA CALCIUM ION × 4 GEL 1-O-OCTYL-2-HEPTYLPHOSPHONYL-SN-GLYCERO-3-PHOSPHOETHANOLAMINE × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.10 Å
3U8B Functionally selective inhibition of Group IIA phospholipase A2 reveals a role for vimentin in regulating arachidonic acid metabolism Deposited 2011-10-16 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 21–144（124 aa）
Not recorded CL CHLORIDE ION × 2 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；0.1 M Tris HCl pH 7.4, 10 mM CaCl2, 0.5 mM Beta-octyl glucoside and 4 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.30 Å R-free 0.257
3U8B Functionally selective inhibition of Group IIA phospholipase A2 reveals a role for vimentin in regulating arachidonic acid metabolism Deposited 2011-10-16 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 21–144（124 aa）
Not recorded CL CHLORIDE ION × 4 CA CALCIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；0.1 M Tris HCl pH 7.4, 10 mM CaCl2, 0.5 mM Beta-octyl glucoside and 4 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.30 Å R-free 0.257
3U8D Functionally selective inhibition of Group IIA phospholipase A2 reveals a role for vimentin in regulating arachidonic acid metabolism Deposited 2011-10-16 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 21–144（124 aa）
Not recorded U8D (3-{[3-(2-amino-2-oxoethyl)-1-benzyl-2-ethyl-1H-indol-5-yl]oxy}propyl)phosphonic acid × 1 CA CALCIUM ION × 2 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；0.1 M Tris-HCl pH 7.4, 10 mM CaCl2, 0.5 mM beta-octyl glucoside and 4 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.80 Å R-free 0.189
3U8D Functionally selective inhibition of Group IIA phospholipase A2 reveals a role for vimentin in regulating arachidonic acid metabolism Deposited 2011-10-16 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 21–144（124 aa）
Not recorded U8D (3-{[3-(2-amino-2-oxoethyl)-1-benzyl-2-ethyl-1H-indol-5-yl]oxy}propyl)phosphonic acid × 1 CA CALCIUM ION × 2 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；0.1 M Tris-HCl pH 7.4, 10 mM CaCl2, 0.5 mM beta-octyl glucoside and 4 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.80 Å R-free 0.189
3U8H Functionally selective inhibition of Group IIA phospholipase A2 reveals a role for vimentin in regulating arachidonic acid metabolism Deposited 2011-10-17 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 21–144（124 aa）
Not recorded BHP (S)-5-(4-BENZYLOXY-PHENYL)-4-(7-PHENYL-HEPTANOYLAMINO)-PENTANOIC ACID × 1 CA CALCIUM ION × 2 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；0.1 M Tris HCl pH 7.4, 10 mM CaCl2, 0.5 mM Beta-octyl glucoside and 4 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.30 Å R-free 0.225
3U8H Functionally selective inhibition of Group IIA phospholipase A2 reveals a role for vimentin in regulating arachidonic acid metabolism Deposited 2011-10-17 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 21–144（124 aa）
Not recorded BHP (S)-5-(4-BENZYLOXY-PHENYL)-4-(7-PHENYL-HEPTANOYLAMINO)-PENTANOIC ACID × 1 CA CALCIUM ION × 2 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；0.1 M Tris HCl pH 7.4, 10 mM CaCl2, 0.5 mM Beta-octyl glucoside and 4 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.30 Å R-free 0.225
3U8H Functionally selective inhibition of Group IIA phospholipase A2 reveals a role for vimentin in regulating arachidonic acid metabolism Deposited 2011-10-17 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 21–144（124 aa）
Chain B 21–144（124 aa）
Not recorded BHP (S)-5-(4-BENZYLOXY-PHENYL)-4-(7-PHENYL-HEPTANOYLAMINO)-PENTANOIC ACID × 2 CA CALCIUM ION × 4 CL CHLORIDE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；0.1 M Tris HCl pH 7.4, 10 mM CaCl2, 0.5 mM Beta-octyl glucoside and 4 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.30 Å R-free 0.225
3U8I Functionally selective inhibition of Group IIA phospholipase A2 reveals a role for vimentin in regulating arachidonic acid metabolism Deposited 2011-10-17 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 21–144（124 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) CA CALCIUM ION × 2 CL CHLORIDE ION × 2 NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；0.1 M Tris HCl pH 7.4, 10 mM CaCl2, 0.5 mM Beta-octyl glucoside and 4 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.10 Å R-free 0.186
3U8I Functionally selective inhibition of Group IIA phospholipase A2 reveals a role for vimentin in regulating arachidonic acid metabolism Deposited 2011-10-17 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 21–144（124 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) CA CALCIUM ION × 2 CL CHLORIDE ION × 2 NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；0.1 M Tris HCl pH 7.4, 10 mM CaCl2, 0.5 mM Beta-octyl glucoside and 4 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.10 Å R-free 0.186
5G3N Discovery of a novel secreted phospholipase A2 (sPLA2) inhibitor. Deposited 2016-04-29 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 21–144（124 aa）
Mutation：YES CA CALCIUM ION × 2 FMT FORMIC ACID × 1 X28 3-(5'-BENZYL-2'-CARBAMOYLBIPHENYL-3-YL)PROPANOIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 3.0-3.5M SODIUM FORMATE AND 100MM HEPES PH 7.5
Resolution 1.80 Å R-free 0.231
5G3N Discovery of a novel secreted phospholipase A2 (sPLA2) inhibitor. Deposited 2016-04-29 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 21–144（124 aa）
Mutation：YES CA CALCIUM ION × 2 FMT FORMIC ACID × 1 X28 3-(5'-BENZYL-2'-CARBAMOYLBIPHENYL-3-YL)PROPANOIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 3.0-3.5M SODIUM FORMATE AND 100MM HEPES PH 7.5
Resolution 1.80 Å R-free 0.231

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

View Construct and Data Evidence
UniProt name PA2GA_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–124； UniProt 21–144

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 1pod

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1pod
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1pod
Deposition date deposition_date1992-09-07
Structure title titleSTRUCTURES OF FREE AND INHIBITED HUMAN SECRETORY PHOSPHOLIPASE A2 FROM INFLAMMATORY EXUDATE
Keywords keywordsHYDROLASE; 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_guinier15.26 Å
Radius of gyration Rg (electron density) rg_electron14.31 Å
Forward intensity I(0) i04543790.00
Molecular weight molecular_weight13973.0 kDa
Excluded volume excluded_volume16982 ų
Envelope volume envelope_volume19397 ų
Hydration-shell volume shell_volume11743 ų
Envelope diameter envelope_diameter48.5 Å
Shell Rg shell_rg19.69 Å
Envelope Rg envelope_rg14.59 Å
Shape Rg shape_rg14.28 Å
Total Rg total_rg15.40 Å
Total atoms total_atoms967
Residues n_residues124
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 dmax49.6 Å
Rg (real space) rg_real15.21 Å
Rg uncertainty (real space) rg_real_error0.20 Å
I(0) (real space) i0_real4.5440e+06
I(0) uncertainty (real space) i0_real_error4.0980e+04
Rg (reciprocal space) rg_reciprocal15.21 Å
I(0) (reciprocal space) i0_reciprocal4544000.0000
Solution quality estimate total_estimate0.8944
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary16.9 Å
Skewness Skewness skewness0.247
Kurtosis Kurtosis kurtosis-0.407
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1127000.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.884; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.979
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1poda_
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_id1podA00
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)