SAXSdb — 2zch

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

Prostate-specific antigen

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain P； UniProt 25–261	Fragment：UNP residues 25-261	monoclonal antibody 8G8F5 Fab × 1 monoclonal antibody 8G8F5 Fab × 1 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

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 2ZCH	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2ZCK Crystal structure of a ternary complex between PSA, a substrat-acyl intermediate and an activating antibody Deposited 2007-11-09	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 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 construct 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 construct 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
9ZJQ Human KLK3 following acylation by CDD-3290 Deposited 2025-12-05	Different construct 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 25–261（237 aa）	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

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 P； 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	2zch
Deposition date deposition_date	2007-11-08
Structure title title	Crystal structure of human prostate specific antigen complexed with an activating antibody
Keywords keywords	;human PSA, kallikrein related peptidases, antibodies, prostate cancer, Glycoprotein, Hydrolase, Polymorphism, Protease, Secreted, Serine protease, Zymogen, IMMUNE SYSTEM ;; IMMUNE SYSTEM
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	33.16 Å
Radius of gyration Rg (electron density) rg_electron	33.26 Å
Forward intensity I(0) i0	91502400.00
Molecular weight molecular_weight	74429.0 kDa
Excluded volume excluded_volume	92355 Å³
Envelope volume envelope_volume	121170 Å³
Hydration-shell volume shell_volume	32898 Å³
Envelope diameter envelope_diameter	131.9 Å
Shell Rg shell_rg	36.97 Å
Envelope Rg envelope_rg	33.57 Å
Shape Rg shape_rg	33.21 Å
Total Rg total_rg	33.72 Å
Total atoms total_atoms	5224
Residues n_residues	654
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	124.8 Å
Rg (real space) rg_real	33.67 Å
Rg uncertainty (real space) rg_real_error	1.23 Å
I(0) (real space) i0_real	9.1500e+07
I(0) uncertainty (real space) i0_real_error	1.7550e+06
Rg (reciprocal space) rg_reciprocal	33.45 Å
I(0) (reciprocal space) i0_reciprocal	91490000.0000
Solution quality estimate total_estimate	0.5684
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	31.2 Å
Skewness Skewness skewness	0.621
Kurtosis Kurtosis kurtosis	-0.214
Angular range angular_range	— – 0.2400 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	18130000.0000
Real-space data points n_real_points	49
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.508; Stabil: 1.000; Sysdev: 0.145; Positv: 1.000; Valcen: 0.429; Smooth: 0.996

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Prostate-specific antigen
Molecular weight formula_weight	26122.0 kDa
EC 编号 ec_number	3.4.21.77
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P
Atom count atom_count	5290

IVGGWECEKHSQPWQVLVASRGRAVCGGVLVHPQWVLTAAHCIRNKSVILLGRHSLFHPEDTGQVFQVSHSFPHPLYDMSLLKNRFLRPGDDSSHDLMLLRLSEPAELTDAVKVMDLPTQEPALGTTCYASGWGSIEPEEFLTPKKLQCVDLHVISNDVCAQVHPQKVTKFMLCAGRWTGGKSTCSGDSGGPLVCNGVLQGITSWGSEPCALPERPSLYTKVVHYRKWIKDTIVANP

Entity 2 Entity 2 polymer

Description description	monoclonal antibody 8G8F5 Fab
Molecular weight formula_weight	23444.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L

DIVLTQSPASLAVSLGQRATISCKASQSVDFDGDSYMNWYQQKPGQPPKLLIFAASNLASGIPARLSGSGSGTDFTLNIQPVEEEDAATYYCQQSNEDPYTFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNR

Entity 3 Entity 3 polymer

Description description	monoclonal antibody 8G8F5 Fab
Molecular weight formula_weight	24366.2 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	H

QVQLQQSGDDLVKPGASVKLSCKASGYTFTTYYINWMRQRPGQGLEWIGRIAPASGTTYSSEMFKDKATLTVDTSSNTAYIQLSSLSSEDSAVYFCARADYGFNSGEAMDYWGQGTSVTVSSAKTTAPPVYPLAPVCGDTTGSSVTLGCLVKGYFPESVTLLWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIVPRDCGCKPC

Entity 4 Entity 4 non-polymer

Description description	2-acetamido-2-deoxy-alpha-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	66

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7. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d2zchh1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.1 — V set domains (antibody variable domain-like)

Domain ID domain_id	d2zchh2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d2zchl1
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.0 — automated matches

Domain ID domain_id	d2zchl2
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.2 — C1 set domains (antibody constant domain-like)

Domain ID domain_id	d2zchp_
Class class	b — All beta proteins
Fold Fold fold	b.47 — Trypsin-like serine proteases
Superfamily Superfamily superfamily	b.47.1 — Trypsin-like serine proteases
Family Family family	b.47.1.2 — Eukaryotic proteases

CATH v4.4 (6 domains)

Domain ID domain_id	2zchH01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2zchH02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2zchL01
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2zchL02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

Domain ID domain_id	2zchP01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

Domain ID domain_id	2zchP02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	10 — Thrombin, subunit H
Homologous superfamily homologous superfamily	10 — Trypsin-like serine proteases

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8. Citations (1)

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Unit-cell length a length_a	87.360 Å
Unit-cell length b length_b	87.360 Å
Unit-cell length c length_c	236.332 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	8

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.830 Å
Low-resolution limit resolution_low	78.810 Å
R factor r_factor	0.2065
R_work r_work	0.2032
R_free r_free	0.2703

fit	/app/data/saxs_computation/zc/2zch/2zch.fit
pddf	/app/data/pr_computation/zc/2zch/2zch.pr.out
profile	/app/data/saxs_computation/zc/2zch/2zch.dat

Crystal structure of human prostate specific antigen complexed with an activating antibody

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

6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

7. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (5 domains)

CATH v4.4 (6 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)