SAXSdb — 1clv

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

PROTEIN (ALPHA-AMYLASE)

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 2–471	Non-standard monomer：Yes (specific site not provided by mmCIF)	PROTEIN (ALPHA-AMYLASE INHIBITOR) × 1 （P80403） CA CALCIUM ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.4；12% PEG 1000, 12% PEG 8000, pH 5.4	Resolution 2.00 Å R-free 0.190

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 1CLV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1JAE STRUCTURE OF TENEBRIO MOLITOR LARVAL ALPHA-AMYLASE Deposited 1997-09-30	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–471（470 aa） Fragment：RESIDUES 1 - 471	Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；200 MM SODIUM ACETATE, 100 MM BISTRIS-HCL PH 6.5 30% W/V PEG 8000	Resolution 1.65 Å R-free 0.206
1TMQ STRUCTURE OF TENEBRIO MOLITOR LARVAL ALPHA-AMYLASE IN COMPLEX WITH RAGI BIFUNCTIONAL INHIBITOR Deposited 1998-01-13	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–471（470 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CL CHLORIDE ION × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions 200MM AMMONIUM PHOSPHATE, 100MM TRIS-HCL, PH 8.5, 50% (W/V) 2-METHYL-2,4- PENTANEDIOL	Resolution 2.50 Å R-free 0.261
1VIW TENEBRIO MOLITOR ALPHA-AMYLASE-INHIBITOR COMPLEX Deposited 1998-07-21	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 2–471（470 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CL CHLORIDE ION × 2 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7	Resolution 3.00 Å R-free 0.291
1VIW TENEBRIO MOLITOR ALPHA-AMYLASE-INHIBITOR COMPLEX Deposited 1998-07-21	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–471（470 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CL CHLORIDE ION × 1 CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7	Resolution 3.00 Å R-free 0.291

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

View Construct and Data Evidence

UniProt name	AMY_TENMO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–471； UniProt 2–471

PROTEIN (ALPHA-AMYLASE INHIBITOR)

OrganismNot specified

UniProt P80403

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 I； UniProt 1–32	Not recorded	PROTEIN (ALPHA-AMYLASE) × 1 （P56634） CA CALCIUM ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 5.4；12% PEG 1000, 12% PEG 8000, pH 5.4	Resolution 2.00 Å R-free 0.190

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 1CLV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1HTX SOLUTION STRUCTURE OF THE MAIN ALPHA-AMYLASE INHIBITOR FROM AMARANTH SEEDS Deposited 2001-01-02	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–32（32 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 2.95；277 K；Pressure ambient NMR measurement conditions pH 2.95；277 K；Pressure ambient NMR sample composition 1.8 mM AAI, 0.05 mM NaN3 \| 90% H2O/10% D2O NMR sample composition 1.8 mM AAI, 0.05 mM NaN3 \| 100% D2O	Resolution not provided
1QFD NMR SOLUTION STRUCTURE OF ALPHA-AMYLASE INHIBITOR (AAI) Deposited 1999-04-08	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–32（32 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；300 K；Ionic strength (raw mmCIF value) 20 mM；Pressure 1 NMR sample composition 90% WATER/10% D2O	Resolution not provided

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

View Construct and Data Evidence

UniProt name	IAAI_AMAHP
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain I； PDBConstruct 1–32； UniProt 1–32

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	1clv
Deposition date deposition_date	1999-05-04
Structure title title	YELLOW MEAL WORM ALPHA-AMYLASE IN COMPLEX WITH THE AMARANTH ALPHA-AMYLASE INHIBITOR
Keywords keywords	INSECT ALPHA-AMYLASE INHIBITOR, AMARANTHUS HYPOCHONDRIACUS, YELLOW MEAL WORM, KNOTTIN, 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	23.74 Å
Radius of gyration Rg (electron density) rg_electron	22.46 Å
Forward intensity I(0) i0	55650700.00
Molecular weight molecular_weight	54863.0 kDa
Excluded volume excluded_volume	67008 Å³
Envelope volume envelope_volume	75820 Å³
Hydration-shell volume shell_volume	27797 Å³
Envelope diameter envelope_diameter	80.3 Å
Shell Rg shell_rg	30.06 Å
Envelope Rg envelope_rg	22.62 Å
Shape Rg shape_rg	22.44 Å
Total Rg total_rg	23.29 Å
Total atoms total_atoms	3854
Residues n_residues	502
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	77.2 Å
Rg (real space) rg_real	23.67 Å
Rg uncertainty (real space) rg_real_error	0.49 Å
I(0) (real space) i0_real	5.5650e+07
I(0) uncertainty (real space) i0_real_error	7.8250e+05
Rg (reciprocal space) rg_reciprocal	23.69 Å
I(0) (reciprocal space) i0_reciprocal	55650000.0000
Solution quality estimate total_estimate	0.8084
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.9 Å
Skewness Skewness skewness	0.315
Kurtosis Kurtosis kurtosis	-0.245
Angular range angular_range	— – 0.3350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	12610000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.836; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	PROTEIN (ALPHA-AMYLASE)
Molecular weight formula_weight	51263.1 kDa
EC 编号 ec_number	3.2.1.1
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4127

QKDANFASGRNSIVHLFEWKWNDIADECERFLQPQGFGGVQISPPNEYLVADGRPWWERYQPVSYIINTRSGDESAFTDMTRRCNDAGVRIYVDAVINHMTGMNGVGTSGSSADHDGMNYPAVPYGSGDFHSPCEVNNYQDADNVRNCELVGLRDLNQGSDYVRGVLIDYMNHMIDLGVAGFRVDAAKHMSPGDLSVIFSGLKNLNTDYGFADGARPFIYQEVIDLGGEAISKNEYTGFGCVLEFQFGVSLGNAFQGGNQLKNLANWGPEWGLLEGLDAVVFVDNHDNQRTGGSQILTYKNPKPYKMAIAFMLAHPYGTTRIMSSFDFTDNDQGPPQDGSGNLISPGINDDNTCSNGYVCEHRWRQVYGMVGFRNAVEGTQVENWWSNDDNQIAFSRGSQGFVAFTNGGDLNQNLNTGLPAGTYCDVISGELSGGSCTGKSVTVGDNGSADISLGSAEDDGVLAIHVNAKL

Entity 2 Entity 2 polymer

Description description	PROTEIN (ALPHA-AMYLASE INHIBITOR)
Molecular weight formula_weight	3595.1 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	I

CIPKWNRCGPKMDGVPCCEPYTCTSDYYGNCS

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	1

Entity 4 Entity 4 non-polymer

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

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	273

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1clva1
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	d1clva2
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	d1clvi_
Class class	g — Small proteins
Fold Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamily	g.3.2 — Plant inhibitors of proteinases and amylases
Family Family family	g.3.2.1 — Plant inhibitors of proteinases and amylases

CATH v4.4 (2 domains)

Domain ID domain_id	1clvA01
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	1clvA02
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	1180 — Golgi alpha-mannosidase II

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8. Citations (1)

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Unit-cell length a length_a	119.250 Å
Unit-cell length b length_b	119.250 Å
Unit-cell length c length_c	64.780 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 61
Space-group number int_tables_number	169
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	—
R_work r_work	0.1610
R_free r_free	0.1900

fit	/app/data/saxs_computation/cl/1clv/1clv.fit
pddf	/app/data/pr_computation/cl/1clv/1clv.pr.out
profile	/app/data/saxs_computation/cl/1clv/1clv.dat

YELLOW MEAL WORM ALPHA-AMYLASE IN COMPLEX WITH THE AMARANTH ALPHA-AMYLASE INHIBITOR

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

PROTEIN (ALPHA-AMYLASE)

State in the Current Structure

Other States of the Same Protein in the Database

PROTEIN (ALPHA-AMYLASE 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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)