SAXSdb — 1htr

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

PROGASTRICSIN (PRO SEGMENT)

Homo sapiens

UniProt P20142

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 60–388 Chain P； UniProt 17–59	Not recorded	No other associated polymer	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.62 Å
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 60–388 Chain P； UniProt 17–59	Not recorded	No other associated polymer	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.62 Å

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 1HTR	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AVF ACTIVATION INTERMEDIATE 2 OF HUMAN GASTRICSIN FROM HUMAN STOMACH Deposited 1997-09-16	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 60–388（329 aa） Chain P 17–42（26 aa）	Not recorded	NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.8；PROTEIN WAS CRYSTALLIZED IN 4M NA FORMATE, 100 MM BIS-TRIS-PROPANE, PH 7.8.	Resolution 2.36 Å R-free 0.282
1AVF ACTIVATION INTERMEDIATE 2 OF HUMAN GASTRICSIN FROM HUMAN STOMACH Deposited 1997-09-16	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain J 60–388（329 aa） Chain Q 17–42（26 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.8；PROTEIN WAS CRYSTALLIZED IN 4M NA FORMATE, 100 MM BIS-TRIS-PROPANE, PH 7.8.	Resolution 2.36 Å R-free 0.282

1 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PEPC_HUMAN
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain P； PDBConstruct 1–43； UniProt 17–59 Author chain B； PDBConstruct 1–329； UniProt 60–388

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	1htr
Deposition date deposition_date	1994-10-21
Structure title title	CRYSTAL AND MOLECULAR STRUCTURES OF HUMAN PROGASTRICSIN AT 1.62 ANGSTROMS RESOLUTION
Keywords keywords	ASPARTYL PROTEASE; ASPARTYL PROTEASE
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	21.44 Å
Radius of gyration Rg (electron density) rg_electron	20.05 Å
Forward intensity I(0) i0	27411300.00
Molecular weight molecular_weight	40552.0 kDa
Excluded volume excluded_volume	50768 Å³
Envelope volume envelope_volume	58084 Å³
Hydration-shell volume shell_volume	23786 Å³
Envelope diameter envelope_diameter	66.2 Å
Shell Rg shell_rg	26.99 Å
Envelope Rg envelope_rg	20.08 Å
Shape Rg shape_rg	20.04 Å
Total Rg total_rg	20.99 Å
Total atoms total_atoms	2863
Residues n_residues	372
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	67.0 Å
Rg (real space) rg_real	21.30 Å
Rg uncertainty (real space) rg_real_error	0.23 Å
I(0) (real space) i0_real	2.7410e+07
I(0) uncertainty (real space) i0_real_error	3.3810e+05
Rg (reciprocal space) rg_reciprocal	21.33 Å
I(0) (reciprocal space) i0_reciprocal	27410000.0000
Solution quality estimate total_estimate	0.8970
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.6 Å
Skewness Skewness skewness	0.176
Kurtosis Kurtosis kurtosis	-0.389
Angular range angular_range	— – 0.3700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7059000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.891; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.995

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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	PROGASTRICSIN (PRO SEGMENT)
Molecular weight formula_weight	5137.1 kDa
EC 编号 ec_number	3.4.23.3
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P
Atom count atom_count	3129

AVVKVPLKKFKSIRETMKEKGLLGEFLRTHKYDPAWKYRFGDL

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 polymer

Description description	GASTRICSIN
Molecular weight formula_weight	35464.9 kDa
EC 编号 ec_number	3.4.23.3
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

SVTYEPMAYMDAAYFGEISIGTPPQNFLVLFDTGSSNLWVPSVYCQSQACTSHSRFNPSESSTYSTNGQTFSLQYGSGSLTGFFGYDTLTVQSIQVPNQEFGLSENEPGTNFVYAQFDGIMGLAYPALSVDEATTAMQGMVQEGALTSPVFSVYLSNQQGSSGGAVVFGGVDSSLYTGQIYWAPVTQELYWQIGIEEFLIGGQASGWCSEGCQAIVDTGTSLLTVPQQYMSALLQATGAQEDEYGQFLVNCNSIQNLPSLTFIINGVEFPLPPSSYILSNNGYCTVGVEPTYLSSQNGQPLWILGDVFLRSYYSVYDLGNNRVGFATAA

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 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	250

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1htr.1
Class class	b — All beta proteins
Fold Fold fold	b.50 — Acid proteases
Superfamily Superfamily superfamily	b.50.1 — Acid proteases
Family Family family	b.50.1.2 — Pepsin-like

CATH v4.4 (3 domains)

Domain ID domain_id	1htrB01
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	70 — Cathepsin D, subunit A; domain 1
Homologous superfamily homologous superfamily	10 — Acid Proteases

Domain ID domain_id	1htrB02
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	70 — Cathepsin D, subunit A; domain 1
Homologous superfamily homologous superfamily	10 — Acid Proteases

Domain ID domain_id	1htrP00
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	140 — Helix Hairpins
Homologous superfamily homologous superfamily	60 —

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8. Citations (2)

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Unit-cell length a length_a	105.310 Å
Unit-cell length b length_b	105.310 Å
Unit-cell length c length_c	70.420 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 42 21 2
Space-group number int_tables_number	94
Crystal system crystal_system	—

Resolution resolution	1.620 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1790
R_work r_work	—
R_free r_free	—

fit	/app/data/saxs_computation/ht/1htr/1htr.fit
pddf	/app/data/pr_computation/ht/1htr/1htr.pr.out
profile	/app/data/saxs_computation/ht/1htr/1htr.dat

CRYSTAL AND MOLECULAR STRUCTURES OF HUMAN PROGASTRICSIN AT 1.62 ANGSTROMS RESOLUTION

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

PROGASTRICSIN (PRO SEGMENT)

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

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (1 domains)

CATH v4.4 (3 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)