SAXSdb — 1ava

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

BARLEY ALPHA-AMYLASE 2(CV MENUET)

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 25–427	Not recorded	BARLEY ALPHA-AMYLASE/SUBTILISIN INHIBITOR × 1 （P07596） CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.7；pH 6.7	Resolution 1.90 Å R-free 0.269
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 25–427	Not recorded	BARLEY ALPHA-AMYLASE/SUBTILISIN INHIBITOR × 1 （P07596） CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.7；pH 6.7	Resolution 1.90 Å R-free 0.269

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 1AVA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AMY CRYSTAL AND MOLECULAR STRUCTURE OF BARLEY ALPHA-AMYLASE Deposited 1994-03-10	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 25–427（403 aa）	Not recorded	CA CALCIUM ION × 3	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.80 Å
1BG9 BARLEY ALPHA-AMYLASE WITH SUBSTRATE ANALOGUE ACARBOSE Deposited 1998-06-05	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 25–427（403 aa）	Not recorded	CA CALCIUM ION × 6 AF1 4,6-dideoxy-4-{[(1S,4S,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.7；pH 6.7	Resolution 2.80 Å R-free 0.249

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

View Construct and Data Evidence

UniProt name	AMY2_HORVU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–403； UniProt 25–427 Author chain B； PDBConstruct 1–403； UniProt 25–427

BARLEY ALPHA-AMYLASE/SUBTILISIN INHIBITOR

OrganismNot specified

UniProt P07596

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 23–203	Not recorded	BARLEY ALPHA-AMYLASE 2(CV MENUET) × 1 （P04063） CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.7；pH 6.7	Resolution 1.90 Å R-free 0.269
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 23–203	Not recorded	BARLEY ALPHA-AMYLASE 2(CV MENUET) × 1 （P04063） CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.7；pH 6.7	Resolution 1.90 Å R-free 0.269

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 1AVA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2IWT Thioredoxin h2 (HvTrxh2) in a mixed disulfide complex with the target protein BASI Deposited 2006-07-04	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 22–203（182 aa）	Mutation：YES	FLC CITRATE ANION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5；0.1 M CITRIC ACID PH 5.0, 12% PEG6000	Resolution 2.30 Å R-free 0.264
3BX1 Complex between the Barley alpha-Amylase/Subtilisin Inhibitor and the subtilisin Savinase Deposited 2008-01-11	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 23–203（181 aa）	Not recorded	CA CALCIUM ION × 2 CL CHLORIDE ION × 15 NA SODIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；291 K；0.1 M sodium acetate buffer pH 5.6 and 4 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.85 Å R-free 0.239
3BX1 Complex between the Barley alpha-Amylase/Subtilisin Inhibitor and the subtilisin Savinase Deposited 2008-01-11	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 23–203（181 aa）	Not recorded	CA CALCIUM ION × 2 CL CHLORIDE ION × 9 NA SODIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；291 K；0.1 M sodium acetate buffer pH 5.6 and 4 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.85 Å R-free 0.239
3BX1 Complex between the Barley alpha-Amylase/Subtilisin Inhibitor and the subtilisin Savinase Deposited 2008-01-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain C 23–203（181 aa） Chain D 23–203（181 aa）	Not recorded	CA CALCIUM ION × 8 CL CHLORIDE ION × 48 NA SODIUM ION × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；291 K；0.1 M sodium acetate buffer pH 5.6 and 4 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 1.85 Å R-free 0.239

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

View Construct and Data Evidence

UniProt name	IAAS_HORVU
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–181； UniProt 23–203 Author chain D； PDBConstruct 1–181； UniProt 23–203

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	1ava
Deposition date deposition_date	1997-09-15
Structure title title	AMY2/BASI PROTEIN-PROTEIN COMPLEX FROM BARLEY SEED
Keywords keywords	HYDROLASE INHIBITION, ENZYME INHIBITOR COMPLEX; HYDROLASE INHIBITION
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	35.87 Å
Radius of gyration Rg (electron density) rg_electron	35.28 Å
Forward intensity I(0) i0	260881000.00
Molecular weight molecular_weight	129910.0 kDa
Excluded volume excluded_volume	161840 Å³
Envelope volume envelope_volume	201970 Å³
Hydration-shell volume shell_volume	47043 Å³
Envelope diameter envelope_diameter	112.3 Å
Shell Rg shell_rg	42.50 Å
Envelope Rg envelope_rg	34.72 Å
Shape Rg shape_rg	35.26 Å
Total Rg total_rg	35.81 Å
Total atoms total_atoms	9184
Residues n_residues	1168
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	114.5 Å
Rg (real space) rg_real	35.79 Å
Rg uncertainty (real space) rg_real_error	0.88 Å
I(0) (real space) i0_real	2.6090e+08
I(0) uncertainty (real space) i0_real_error	4.1450e+06
Rg (reciprocal space) rg_reciprocal	35.84 Å
I(0) (reciprocal space) i0_reciprocal	260900000.0000
Solution quality estimate total_estimate	0.9074
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	41.6 Å
Skewness Skewness skewness	0.198
Kurtosis Kurtosis kurtosis	-0.662
Angular range angular_range	— – 0.2200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	63220000.0000
Real-space data points n_real_points	45
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.945; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.962

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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	BARLEY ALPHA-AMYLASE 2(CV MENUET)
Molecular weight formula_weight	44986.4 kDa
EC 编号 ec_number	3.2.1.1
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	9932

QVLFQGFNWESWKHNGGWYNFLMGKVDDIAAAGITHVWLPPASQSVAEQGYMPGRLYDLDASKYGNKAQLKSLIGALHGKGVKAIADIVINHRTAEHKDGRGIYCIFEGGTPDARLDWGPHMICRDDRPYADGTGNPDTGADFGAAPDIDHLNLRVQKELVEWLNWLKADIGFDGWRFDFAKGYSADVAKIYIDRSEPSFAVAEIWTSLAYGGDGKPNLNQDQHRQELVNWVDKVGGKGPATTFDFTTKGILNVAVEGELWRLRGTDGKAPGMIGWWPAKAVTFVDNHDTGSTQHMWPFPSDRVMQGYAYILTHPGTPCIFYDHFFDWGLKEEIDRLVSVRTRHGIHNESKLQIIEADADLYLAEIDGKVIVKLGPRYDVGNLIPGGFKVAAHGNDYAVWEKI

Entity 2 Entity 2 polymer

Description description	BARLEY ALPHA-AMYLASE/SUBTILISIN INHIBITOR
Molecular weight formula_weight	19908.3 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

ADPPPVHDTDGHELRADANYYVLSANRAHGGGLTMAPGHGRHCPLFVSQDPNGQHDGFPVRITPYGVAPSDKIIRLSTDVRISFRAYTTCLQSTEWHIDSELAAGRRHVITGPVKDPSPSGRENAFRIEKYSGAEVHEYKLMSCGDWCQDLGVFRDLKGGAWFLGATEPYHVVVFKKAPPA

Entity 3 Entity 3 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	748

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7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1avaa1
Class class	b — All beta proteins
Fold Fold fold	b.71 — Glycosyl hydrolase domain
Superfamily Superfamily superfamily	b.71.1 — Glycosyl hydrolase domain
Family Family family	b.71.1.1 — alpha-Amylases, C-terminal beta-sheet domain

Domain ID domain_id	d1avaa2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.8 — (Trans)glycosidases
Family Family family	c.1.8.1 — Amylase, catalytic domain

Domain ID domain_id	d1avab1
Class class	b — All beta proteins
Fold Fold fold	b.71 — Glycosyl hydrolase domain
Superfamily Superfamily superfamily	b.71.1 — Glycosyl hydrolase domain
Family Family family	b.71.1.1 — alpha-Amylases, C-terminal beta-sheet domain

Domain ID domain_id	d1avab2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamily	c.1.8 — (Trans)glycosidases
Family Family family	c.1.8.1 — Amylase, catalytic domain

Domain ID domain_id	d1avac_
Class class	b — All beta proteins
Fold Fold fold	b.42 — beta-Trefoil
Superfamily Superfamily superfamily	b.42.4 — STI-like
Family Family family	b.42.4.1 — Kunitz (STI) inhibitors

Domain ID domain_id	d1avad_
Class class	b — All beta proteins
Fold Fold fold	b.42 — beta-Trefoil
Superfamily Superfamily superfamily	b.42.4 — STI-like
Family Family family	b.42.4.1 — Kunitz (STI) inhibitors

CATH v4.4 (6 domains)

Domain ID domain_id	1avaA01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	80 — Glycosidases

Domain ID domain_id	1avaA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1180 — Golgi alpha-mannosidase II

Domain ID domain_id	1avaB01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	20 — TIM Barrel
Homologous superfamily homologous superfamily	80 — Glycosidases

Domain ID domain_id	1avaB02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1180 — Golgi alpha-mannosidase II

Domain ID domain_id	1avaC00
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	1avaD00
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

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8. Citations (2)

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Unit-cell length a length_a	74.500 Å
Unit-cell length b length_b	96.180 Å
Unit-cell length c length_c	170.150 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.2080
R_work r_work	0.2080
R_free r_free	0.2690

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

AMY2/BASI PROTEIN-PROTEIN COMPLEX FROM BARLEY SEED

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

BARLEY ALPHA-AMYLASE 2(CV MENUET)

State in the Current Structure

Other States of the Same Protein in the Database

BARLEY ALPHA-AMYLASE/SUBTILISIN INHIBITOR

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) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)