SAXSdb — 2pzd

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

Serine protease HTRA2

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 359–458 Chain B； UniProt 359–458	Not recorded	EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 5.6；292 K；0.1 M sodium citrate, 1.0 M monoammonium dihydrogen phosphate, pH 5.6, VAPOR DIFFUSION, temperature 292K	Resolution 2.75 Å R-free 0.254

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 2PZD	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1LCY Crystal Structure of the Mitochondrial Serine Protease HtrA2 Deposited 2002-04-07	Different construct 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 134–458（325 aa）	Mutation：S173A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；295 K；lithium sulfate, sodium chloride, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.00 Å R-free 0.274
1LCY Crystal Structure of the Mitochondrial Serine Protease HtrA2 Deposited 2002-04-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 134–458（325 aa）	Mutation：S173A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.8；295 K；lithium sulfate, sodium chloride, pH 5.8, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.00 Å R-free 0.274
5FHT HtrA2 protease mutant V226K Deposited 2015-12-22	Different construct 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 134–458（325 aa）	Not recorded	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 CL CHLORIDE ION × 1 K POTASSIUM ION × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；MES, NaCl, KH2PO4, NaH2PO4	Resolution 1.95 Å R-free 0.228
5M3N HTRA2 wild-type structure Deposited 2016-10-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 134–458（325 aa）	Not recorded	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6；293 K；Crystals were grown using the sitting drop vapor-diffusion method by mixing equal volumes of protein (10-15 mg/mL) and reservoir solution containing 0.1 M MES pH 6.0, 1 M LiCl, and 15-20% (w/v) PEG-6000	Resolution 1.65 Å R-free 0.175
5M3O HTRA2 A141S mutant structure Deposited 2016-10-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 134–458（325 aa）	Mutation：Mutation A141S	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M MES pH 6.0, 1 M LiCl, and 15-20% (w/v) PEG-6000	Resolution 1.70 Å R-free 0.200
5TNY HTRA2 G399S mutant Deposited 2016-10-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 134–458（325 aa）	Mutation：G399S	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.1 M MES pH 6.0, 1 M LiCl, and 15-20% (w/v) PEG-6000	Resolution 1.70 Å R-free 0.187
5TNZ HtrA2 S142D mutant Deposited 2016-10-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 134–458（325 aa） Fragment：UNP residues 134-458	Mutation：S142D	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 3 NA SODIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M MES pH 6.0, 1 M LiCl, and 15-20% (w/v) PEG-6000	Resolution 1.75 Å R-free 0.172
5TO0 HTRA2 S276C mutant Deposited 2016-10-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 134–458（325 aa）	Mutation：Mutation S276C	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M MES pH 6.0, 1 M LiCl, and 15-20% (w/v) PEG-6000	Resolution 1.90 Å R-free 0.177
5TO1 HtrA2 exposed (L266R, F303A) mutant Deposited 2016-10-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 134–458（325 aa）	Mutation：L266R and F303A	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 3 CL CHLORIDE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M MES pH 6.0, 1 M LiCl, and 15-20% (w/v) PEG-6000	Resolution 1.69 Å R-free 0.198
5WYN HtrA2 Pathogenic Mutant Deposited 2017-01-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 134–458（325 aa）	Mutation：S143C,Y295W	CL CHLORIDE ION × 18 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；Sodium phosphate monobasic monohydrate Potassium phosphate monobasic Sodium chloride	Resolution 2.05 Å R-free 0.185
7VGE Structure of the PDZ deleted variant of HtrA2 protease (S306A) Deposited 2021-09-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 140–342（203 aa） Chain B 140–342（203 aa） Chain C 140–342（203 aa）	Mutation：S306A Mutation：S306A Mutation：S306A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；290 K；0.5 M Sodium acetate trihydrate pH 6.0, 2.0 M Sodium formate, 3% glycerol	Resolution 4.00 Å R-free 0.336
7VGE Structure of the PDZ deleted variant of HtrA2 protease (S306A) Deposited 2021-09-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain D 140–341（202 aa） Chain E 140–340（201 aa） Chain F 140–341（202 aa）	Mutation：S306A Mutation：S306A Mutation：S306A	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；290 K；0.5 M Sodium acetate trihydrate pH 6.0, 2.0 M Sodium formate, 3% glycerol	Resolution 4.00 Å R-free 0.336
8AUK Cryo-EM structure of human BIRC6 in complex with HTRA2. Deposited 2022-08-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 134–458（325 aa） Chain D 134–458（325 aa） Chain E 134–458（325 aa）	Mutation：S306A Mutation：S306A Mutation：S306A	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.20 Å
8E2K Cryo-EM structure of BIRC6/HtrA2-S306A Deposited 2022-08-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain X 134–458（325 aa） Chain Y 134–458（325 aa） Chain Z 134–458（325 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.21 Å

12 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	HTRA2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–104； UniProt 359–458 Author chain B； PDBConstruct 5–104； UniProt 359–458

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	2pzd
Deposition date deposition_date	2007-05-17
Structure title title	Crystal Structure of the HtrA2/Omi PDZ Domain Bound to a Phage-Derived Ligand (WTMFWV)
Keywords keywords	PDZ domain, serine protease, apoptosis, mitochondria, peptide-binding module, HYDROLASE; 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	20.32 Å
Radius of gyration Rg (electron density) rg_electron	19.09 Å
Forward intensity I(0) i0	9977130.00
Molecular weight molecular_weight	23972.0 kDa
Excluded volume excluded_volume	30306 Å³
Envelope volume envelope_volume	37010 Å³
Hydration-shell volume shell_volume	16683 Å³
Envelope diameter envelope_diameter	64.8 Å
Shell Rg shell_rg	24.49 Å
Envelope Rg envelope_rg	19.16 Å
Shape Rg shape_rg	19.09 Å
Total Rg total_rg	19.93 Å
Total atoms total_atoms	1686
Residues n_residues	212
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	65.5 Å
Rg (real space) rg_real	20.29 Å
Rg uncertainty (real space) rg_real_error	0.34 Å
I(0) (real space) i0_real	9.9770e+06
I(0) uncertainty (real space) i0_real_error	1.1310e+05
Rg (reciprocal space) rg_reciprocal	20.30 Å
I(0) (reciprocal space) i0_reciprocal	9977000.0000
Solution quality estimate total_estimate	0.7102
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.6 Å
Skewness Skewness skewness	0.268
Kurtosis Kurtosis kurtosis	-0.549
Angular range angular_range	— – 0.3900 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2940000.0000
Real-space data points n_real_points	71
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.886; Stabil: 1.000; Sysdev: 0.193; Positv: 1.000; Valcen: 0.993; Smooth: 0.998

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Serine protease HTRA2
Molecular weight formula_weight	12593.5 kDa
EC 编号 ec_number	3.4.21.108
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	1695

GSHMRRYIGVMMLTLSPSILAELQLREPSFPDVQHGVLIHKVILGSPAHRAGLRPGDVILAIGEQMVQNAEDVYEAVRTQSQLAVQIRRGRETLTLYVTPEVTEGGGWTMFWV

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	Escherichia coli

Entity 2 Entity 2 non-polymer

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

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	9

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2pzda_
Class class	b — All beta proteins
Fold Fold fold	b.36 — PDZ domain-like
Superfamily Superfamily superfamily	b.36.1 — PDZ domain-like
Family Family family	b.36.1.0 — automated matches

Domain ID domain_id	d2pzdb_
Class class	b — All beta proteins
Fold Fold fold	b.36 — PDZ domain-like
Superfamily Superfamily superfamily	b.36.1 — PDZ domain-like
Family Family family	b.36.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	2pzdA01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	42 — Pdz3 Domain
Homologous superfamily homologous superfamily	10 — PDZ domain

Domain ID domain_id	2pzdB01
Class class	2 — Mainly Beta
Architecture architecture	30 — Roll
Topology topology	42 — Pdz3 Domain
Homologous superfamily homologous superfamily	10 — PDZ domain

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8. Citations (1)

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Unit-cell length a length_a	90.105 Å
Unit-cell length b length_b	90.105 Å
Unit-cell length c length_c	83.516 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	16

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

Resolution resolution	2.750 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2100
R_work r_work	0.2080
R_free r_free	0.2540

fit	/app/data/saxs_computation/pz/2pzd/2pzd.fit
pddf	/app/data/pr_computation/pz/2pzd/2pzd.pr.out
profile	/app/data/saxs_computation/pz/2pzd/2pzd.dat

Crystal Structure of the HtrA2/Omi PDZ Domain Bound to a Phage-Derived Ligand (WTMFWV)

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

Serine protease HTRA2

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