SAXSdb — 1db5

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

PROTEIN (PHOSPHOLIPASE A2)

Homo sapiens

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 21–144	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

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 1DB5	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 oligomeric state 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 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 oligomeric state Different ligand/ion Different experimental conditions 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 oligomeric state Different ligand/ion Different experimental conditions 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 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	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 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
1DCY CRYSTAL STRUCTURE OF HUMAN S-PLA2 IN COMPLEX WITH INDOLE 3 ACTIVE SITE INHIBITOR Deposited 1999-11-05	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 oligomeric state 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 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 oligomeric state 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 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 oligomeric state Different ligand/ion Different experimental conditions 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 oligomeric state Different ligand/ion Different experimental conditions 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 ligand/ion 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 ligand/ion 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 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：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
1POD STRUCTURES OF FREE AND INHIBITED HUMAN SECRETORY PHOSPHOLIPASE A2 FROM INFLAMMATORY EXUDATE Deposited 1992-09-07	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 21–144（124 aa）	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.10 Å
1POE STRUCTURES OF FREE AND INHIBITED HUMAN SECRETORY PHOSPHOLIPASE A2 FROM INFLAMMATORY EXUDATE Deposited 1992-09-07	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 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 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 oligomeric state 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 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 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 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 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 oligomeric state 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 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 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 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 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1db5
Deposition date deposition_date	1999-11-02
Structure title title	HUMAN S-PLA2 IN COMPLEX WITH INDOLE 6
Keywords keywords	S-PLA2; STRUCTURE-BASED DRUG DESIGN, HYDROLASE/HYDROLASE INHIBITOR, HYDROLASE-HYDROLASE INHIBITOR complex; HYDROLASE/HYDROLASE INHIBITOR
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	15.23 Å
Radius of gyration Rg (electron density) rg_electron	14.27 Å
Forward intensity I(0) i0	4651690.00
Molecular weight molecular_weight	14394.0 kDa
Excluded volume excluded_volume	17561 Å³
Envelope volume envelope_volume	19724 Å³
Hydration-shell volume shell_volume	11891 Å³
Envelope diameter envelope_diameter	52.8 Å
Shell Rg shell_rg	19.89 Å
Envelope Rg envelope_rg	14.70 Å
Shape Rg shape_rg	14.25 Å
Total Rg total_rg	15.39 Å
Total atoms total_atoms	996
Residues n_residues	124
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	55.1 Å
Rg (real space) rg_real	15.19 Å
Rg uncertainty (real space) rg_real_error	0.34 Å
I(0) (real space) i0_real	4.6520e+06
I(0) uncertainty (real space) i0_real_error	5.2510e+04
Rg (reciprocal space) rg_reciprocal	15.20 Å
I(0) (reciprocal space) i0_reciprocal	4652000.0000
Solution quality estimate total_estimate	0.8436
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	16.7 Å
Skewness Skewness skewness	0.283
Kurtosis Kurtosis kurtosis	-0.321
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1248000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.688; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.900; Smooth: 1.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	PROTEIN (PHOSPHOLIPASE A2)
Molecular weight formula_weight	13945.0 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	1034

NLVNFHRMIKLTTGKEAALSYGFYGCHCGVGGRGSPKDATDRCCVTHDCCYKRLEKRGCGTKFLSYKFSNSGSRITCAKQDSCRSQLCECDKAAATCFARNKTTYNKKYQYYSNKHCRGSTPRC

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606

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	2

Entity 3 Entity 3 non-polymer

Description description	4-(1-BENZYL-3-CARBAMOYLMETHYL-2-METHYL-1H-INDOL-5-YLOXY)-BUTYRIC ACID
Molecular weight formula_weight	380.4 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	38

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1db5a_
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	1db5A00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	90 — Phospholipase A2
Homologous superfamily homologous superfamily	10 — Phospholipase A2 domain

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8. Citations (1)

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Unit-cell length a length_a	76.360 Å
Unit-cell length b length_b	76.360 Å
Unit-cell length c length_c	91.530 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	12

Space group space_group	P 61 2 2
Space-group number int_tables_number	178
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1960
R_work r_work	0.1960
R_free r_free	0.2400

fit	/app/data/saxs_computation/db/1db5/1db5.fit
pddf	/app/data/pr_computation/db/1db5/1db5.pr.out
profile	/app/data/saxs_computation/db/1db5/1db5.dat

HUMAN S-PLA2 IN COMPLEX WITH INDOLE 6

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

PROTEIN (PHOSPHOLIPASE A2)

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