SAXSdb — 1bk9

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

PHOSPHOLIPASE A2

OrganismNot specified

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–124	Not recorded	CA CALCIUM ION × 1 PBP p-Bromophenacyl bromide × 1 BU1 1,4-BUTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；pH 6.5	Resolution 2.00 Å R-free 0.226

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 1BK9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1M8R Crystal Structures of Cadmium-binding Acidic Phospholipase A2 from the Venom of Agkistrodon halys pallas at 1.9 Resolution (crystal grown at pH 7.4) Deposited 2002-07-25	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–124（124 aa）	Not recorded	CD CADMIUM ION × 1 BU1 1,4-BUTANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；293 K；10%(v/v) 1,4-butyldiol, 0.01M CdCl2, 0.1M Na(CH3)2AsO, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.210
1M8S Crystal Structures of Cadmium-binding Acidic Phospholipase A2 from the Venom of Agkistrodon halys pallas at 1.9 Resolution (crystal grown at pH 5.9) Deposited 2002-07-25	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–124（124 aa）	Not recorded	CD CADMIUM ION × 1 BU1 1,4-BUTANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.9；293 K；10%(v/v) 1,4-butyldiol, 0.01M CdCl2, 0.1M Na(CH3)2AsO, pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.90 Å R-free 0.209
1PSJ ACIDIC PHOSPHOLIPASE A2 FROM AGKISTRODON HALYS PALLAS Deposited 1995-05-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–124（124 aa）	Not recorded	CA CALCIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å R-free 0.228

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PA21B_AGKHP
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–124； UniProt 1–124

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	1bk9
Deposition date deposition_date	1998-07-16
Structure title title	PHOSPHOLIPASE A2 MODIFIED BY PBPB
Keywords keywords	HYDROLASE, PHOSPHOLIPASE A2, PLATELET AGGREGATION INHIBITOR, PBPB; HYDROLASE
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	15.49 Å
Radius of gyration Rg (electron density) rg_electron	14.57 Å
Forward intensity I(0) i0	4568530.00
Molecular weight molecular_weight	14297.0 kDa
Excluded volume excluded_volume	17401 Å³
Envelope volume envelope_volume	19663 Å³
Hydration-shell volume shell_volume	11718 Å³
Envelope diameter envelope_diameter	52.7 Å
Shell Rg shell_rg	20.03 Å
Envelope Rg envelope_rg	15.02 Å
Shape Rg shape_rg	14.57 Å
Total Rg total_rg	15.60 Å
Total atoms total_atoms	1199
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	53.4 Å
Rg (real space) rg_real	15.48 Å
Rg uncertainty (real space) rg_real_error	0.38 Å
I(0) (real space) i0_real	4.5690e+06
I(0) uncertainty (real space) i0_real_error	5.7010e+04
Rg (reciprocal space) rg_reciprocal	15.48 Å
I(0) (reciprocal space) i0_reciprocal	4569000.0000
Solution quality estimate total_estimate	0.8632
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	16.9 Å
Skewness Skewness skewness	0.338
Kurtosis Kurtosis kurtosis	-0.261
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1233000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.774; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.944; Smooth: 0.952

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	PHOSPHOLIPASE A2
Molecular weight formula_weight	13988.8 kDa
EC 编号 ec_number	3.1.1.4
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1457

SLIQFETLIMKVAKKSGMFWYSNYGCYCGWGGQGRPQDATDRCCFVHDCCYGKVTGCDPKMDVYSFSEENGDIVCGGDDPCKKEICECDRAAAICFRDNLTLYNDKKYWAFGAKNCPQEESEPC

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	p-Bromophenacyl bromide
Molecular weight formula_weight	277.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	1,4-BUTANEDIOL
Molecular weight formula_weight	90.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

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

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1bk9a_
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	1bk9A00
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	82.820 Å
Unit-cell length b length_b	82.820 Å
Unit-cell length c length_c	32.800 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 61
Space-group number int_tables_number	169
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	6.000 Å
R factor r_factor	0.1530
R_work r_work	0.1530
R_free r_free	0.2260

fit	/app/data/saxs_computation/bk/1bk9/1bk9.fit
pddf	/app/data/pr_computation/bk/1bk9/1bk9.pr.out
profile	/app/data/saxs_computation/bk/1bk9/1bk9.dat

PHOSPHOLIPASE A2 MODIFIED BY PBPB

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

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