SAXSdb — 9zjq

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

Prostate-specific antigen

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 25–261	Not recorded	A1C2U 1H-1,3-benzimidazole-5-carbaldehyde × 1 EDO 1,2-ETHANEDIOL × 5	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；1.4 M sodium malonate pH 7.0. Protein (30 mg/mL) was co-crystallized as 1 uL sitting drop (1:1 protein:precipitant)	Resolution 2.20 Å R-free 0.232

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 9ZJQ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2ZCH Crystal structure of human prostate specific antigen complexed with an activating antibody Deposited 2007-11-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain P 25–261（237 aa） Fragment：UNP residues 25-261	Not recorded	NDG 2-acetamido-2-deoxy-alpha-D-glucopyranose × 2 CL CHLORIDE ION × 1 PO4 PHOSPHATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；14% MPEG 550, 100mM HEPES, pH7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.83 Å R-free 0.270
2ZCK Crystal structure of a ternary complex between PSA, a substrat-acyl intermediate and an activating antibody Deposited 2007-11-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain P 25–261（237 aa） Fragment：UNP residues 25-261	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；crystal grown in 14% MPEG550, 100mM HEPES (pH7.2), then soaked in PEG400, 100mM Tris-HCl (pH7.3), 10mM ZnCl2, 0.28 mg/ml Mu-KGISSQY-AFC, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.10 Å R-free 0.275
2ZCL Crystal structure of human prostate specific antigen complexed with an activating antibody Deposited 2007-11-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain P 25–261（237 aa） Fragment：UNP residues 25-261	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.2；293 K；crystals grown in 14% MPEG550, 100mM HEPES (pH7.2), then soaked in 33% PEG400, 100mM MES (pH5.5), 10mM ZnCl2, 0.28mg/ml Mu-KGISSQY-AFC, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.25 Å R-free 0.251
3QUM Crystal structure of human prostate specific antigen (PSA) in Fab sandwich with a high affinity and a PCa selective antibody Deposited 2011-02-24	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain P 25–261（237 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；Protein solution: 20 ul 5D3D11 at 10.7 mg/ml and 10 ul PSA at 5 mg/ml + 31 ul 5D5A5 at 6.7mg/ml in PBS. against a precipitant of 10% PEG 4,000, 20% ethylene glycol, 100 mM Na,K phosphate. Drops consisted of 1 ul protein + precipitant equilibrated by vapor diffusion. Streak seeding and macro seeding were used, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 3.20 Å R-free 0.294
3QUM Crystal structure of human prostate specific antigen (PSA) in Fab sandwich with a high affinity and a PCa selective antibody Deposited 2011-02-24	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 5 PDB declaration: pentameric	Chain Q 25–261（237 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；295 K；Protein solution: 20 ul 5D3D11 at 10.7 mg/ml and 10 ul PSA at 5 mg/ml + 31 ul 5D5A5 at 6.7mg/ml in PBS. against a precipitant of 10% PEG 4,000, 20% ethylene glycol, 100 mM Na,K phosphate. Drops consisted of 1 ul protein + precipitant equilibrated by vapor diffusion. Streak seeding and macro seeding were used, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K	Resolution 3.20 Å R-free 0.294

4 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	KLK3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–237； UniProt 25–261

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	9zjq
Deposition date deposition_date	2025-12-05
最后修订 last_revision	2025-12-24
Structure title title	Human KLK3 following acylation by CDD-3290
Keywords keywords	Protease, inhibitor, fertility, contraception, cancer, HYDROLASE-INHIBITOR complex; 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	17.74 Å
Radius of gyration Rg (electron density) rg_electron	16.89 Å
Forward intensity I(0) i0	23512300.00
Molecular weight molecular_weight	24674.0 kDa
Excluded volume excluded_volume	23816 Å³
Envelope volume envelope_volume	37675 Å³
Hydration-shell volume shell_volume	18224 Å³
Envelope diameter envelope_diameter	59.1 Å
Shell Rg shell_rg	23.52 Å
Envelope Rg envelope_rg	17.23 Å
Shape Rg shape_rg	16.91 Å
Total Rg total_rg	17.62 Å
Total atoms total_atoms	1863
Residues n_residues	241
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	60.3 Å
Rg (real space) rg_real	17.62 Å
Rg uncertainty (real space) rg_real_error	0.39 Å
I(0) (real space) i0_real	2.3510e+07
I(0) uncertainty (real space) i0_real_error	2.7230e+05
Rg (reciprocal space) rg_reciprocal	17.63 Å
I(0) (reciprocal space) i0_reciprocal	23510000.0000
Solution quality estimate total_estimate	0.7810
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	21.7 Å
Skewness Skewness skewness	0.171
Kurtosis Kurtosis kurtosis	-0.371
Angular range angular_range	— – 0.4500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7149000.0000
Real-space data points n_real_points	76
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.721; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; 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)

Entity 1 Entity 1 polymer

Description description	Prostate-specific antigen
Molecular weight formula_weight	27731.7 kDa
EC 编号 ec_number	3.4.21.77
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	1948

IVGGWECEKHSQPWQVLVASRGRAVCGGVLVHPQWVLTAAHCIRNKSVILLGRHSLFHPEDTGQVFQVSHSFPHPLYDMSLLKNRFLRPGDDSSHDLMLLRLSEPAELTDAVKVMDLPTQEPALGTTCYASGWGSIEPEEFLTPKKLQCVDLHVISNDVCAQVHPQKVTKFMLCAGRWTGGKSTCSGDSGGPLVCNGVLQGITSWGSEPCALPERPSLYTKVVHYRKWIKDTIVANPEFVEHHHHHHHH

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 Entity 2 non-polymer

Description description	1H-1,3-benzimidazole-5-carbaldehyde
Molecular weight formula_weight	146.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	80

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8. Citations (1)

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Unit-cell length a length_a	48.081 Å
Unit-cell length b length_b	56.880 Å
Unit-cell length c length_c	105.243 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	28.460 Å
R factor r_factor	0.2004
R_work r_work	0.1991
R_free r_free	0.2317

fit	/app/data/saxs_computation/zj/9zjq/9zjq.fit
pddf	/app/data/pr_computation/zj/9zjq/9zjq.pr.out
profile	/app/data/saxs_computation/zj/9zjq/9zjq.dat

Human KLK3 following acylation by CDD-3290

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

Prostate-specific antigen

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