SAXSdb — 1avf

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

GASTRICSIN

OrganismNot specified

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 60–388 Chain P； UniProt 17–42	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
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain J； UniProt 60–388 Chain Q； UniProt 17–42	Not recorded	No other associated polymer	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

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 1AVF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1HTR CRYSTAL AND MOLECULAR STRUCTURES OF HUMAN PROGASTRICSIN AT 1.62 ANGSTROMS RESOLUTION Deposited 1994-10-21	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain B 60–388（329 aa） Chain P 17–59（43 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.62 Å
1HTR CRYSTAL AND MOLECULAR STRUCTURES OF HUMAN PROGASTRICSIN AT 1.62 ANGSTROMS RESOLUTION Deposited 1994-10-21	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 60–388（329 aa） Chain P 17–59（43 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.62 Å

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 1–26； UniProt 17–42 Author chain Q； PDBConstruct 1–26； UniProt 17–42 Author chain A； PDBConstruct 1–329； UniProt 60–388 Author chain J； 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	1avf
Deposition date deposition_date	1997-09-16
Structure title title	ACTIVATION INTERMEDIATE 2 OF HUMAN GASTRICSIN FROM HUMAN STOMACH
Keywords keywords	ASPARTYL PROTEASE, GASTRICSIN, ASPARTIC PROTEINASE, INTERMEDIATE, ACTIVATION, ACID; 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	32.27 Å
Radius of gyration Rg (electron density) rg_electron	31.86 Å
Forward intensity I(0) i0	84410500.00
Molecular weight molecular_weight	73983.0 kDa
Excluded volume excluded_volume	92658 Å³
Envelope volume envelope_volume	116950 Å³
Hydration-shell volume shell_volume	31667 Å³
Envelope diameter envelope_diameter	111.5 Å
Shell Rg shell_rg	37.29 Å
Envelope Rg envelope_rg	31.88 Å
Shape Rg shape_rg	31.86 Å
Total Rg total_rg	32.34 Å
Total atoms total_atoms	5219
Residues n_residues	688
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	112.0 Å
Rg (real space) rg_real	32.56 Å
Rg uncertainty (real space) rg_real_error	1.34 Å
I(0) (real space) i0_real	8.4410e+07
I(0) uncertainty (real space) i0_real_error	1.4880e+06
Rg (reciprocal space) rg_reciprocal	32.44 Å
I(0) (reciprocal space) i0_reciprocal	84400000.0000
Solution quality estimate total_estimate	0.8480
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	29.7 Å
Skewness Skewness skewness	0.510
Kurtosis Kurtosis kurtosis	-0.333
Angular range angular_range	— – 0.2450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	16300000.0000
Real-space data points n_real_points	50
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.762; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.810; Smooth: 0.928

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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	GASTRICSIN
Molecular weight formula_weight	2983.7 kDa
EC 编号 ec_number	3.4.23.3
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P,Q
Atom count atom_count	5686

AVVKVPLKKFKSIRETMKEKGLLGEF

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	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,J

SVTYEPMAYMDAAYFGEISIGTPPQNFLVLFDTGSSNLWVPSVYCQSQACTSHSRFNPSESSTYSTNGQTFSLQYGSGSLTGFFGYDTLTVQSIQVPNQEFGLSENEPGTNFVYAQFDGIMGLAYPALSVDEATTAMQGMVQEGALTSPVFSVYLSNQQGSSGGAVVFGGVDSSLYTGQIYWAPVTQELYWQIGIEEFLIGGQASGWCSEGCQAIVDTGTSLLTVPQQYMSALLQATGAQEDEYGQFLVNCNSIQNLPSLTFIINGVEFPLPPSSYILSNNGYCTVGVEPTYLSSQNGQPLWILGDVFLRSYYSVYDLGNNRVGFATAA

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	467

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7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1avf.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

Domain ID domain_id	d1avf.2
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 (4 domains)

Domain ID domain_id	1avfA01
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	1avfA02
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	1avfJ01
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	1avfJ02
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

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8. Citations (1)

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Unit-cell length a length_a	156.260 Å
Unit-cell length b length_b	50.410 Å
Unit-cell length c length_c	125.180 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	117.62 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.360 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2270
R_work r_work	0.2270
R_free r_free	0.2820

fit	/app/data/saxs_computation/av/1avf/1avf.fit
pddf	/app/data/pr_computation/av/1avf/1avf.pr.out
profile	/app/data/saxs_computation/av/1avf/1avf.dat

ACTIVATION INTERMEDIATE 2 OF HUMAN GASTRICSIN FROM HUMAN STOMACH

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

GASTRICSIN

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Fold Classification (SCOP + CATH) 6 domains

SCOP 2.08 (2 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)