SAXSdb — 1smd

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

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 17–511	Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.60 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 1SMD	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1C8Q STRUCTURE SOLUTION AND REFINEMENT OF THE RECOMBINANT HUMAN SALIVARY AMYLASE Deposited 2000-06-08	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 16–511（496 aa）	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 VAPOR DIFFUSION, HANGING DROP；pH 9；273 K；10 mM Tris- HCL containing 5 mM CaCl2, 44% MPD, protein concentration 20 mg/ml, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 273K	Resolution 2.30 Å R-free 0.216
1JXJ Role of mobile loop in the mechanism of human salivary amylase Deposited 2001-09-07	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 16–511（496 aa）	Mutation：W58L 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 VAPOR DIFFUSION, HANGING DROP；pH 9；298 K；MPD, calcium chloride, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K, temperature 298.0K	Resolution 1.99 Å R-free 0.198
1JXK Role of ethe mobile loop in the mehanism of human salivary amylase Deposited 2001-09-07	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 16–511（496 aa） Fragment：lacking the loop residues 306-310	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 VAPOR DIFFUSION, HANGING DROP；pH 9；298 K；MPD, calcium chloride, pH 9.0, VAPOR DIFFUSION, HANGING DROP at 298K	Resolution 1.90 Å R-free 0.200
1MFU Probing the role of a mobile loop in human salivary amylase: Structural studies on the loop-deleted mutant Deposited 2002-08-13	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 17–511（495 aa）	Mutation：deletion of residues 306 through 310 Non-standard monomer：Yes (specific site not provided by mmCIF)	HMC 5-HYDROXYMETHYL-CHONDURITOL × 4 GLC alpha-D-glucopyranose × 1 CA CALCIUM ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions soaking with acarbose at 1 mM concentration for 24 hours；pH 9；298 K；40% mpd, pH 9.0, soaking with acarbose at 1 mM concentration for 24 hours, temperature 298K	Resolution 2.00 Å R-free 0.201
1MFV Probing the role of a mobile loop in human slaivary amylase: Structural studies on the loop-deleted enzyme Deposited 2002-08-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 17–511（495 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	HMC 5-HYDROXYMETHYL-CHONDURITOL × 2 CA CALCIUM ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions vapordiffusion, combined with soaking with inhibitor at 1 mM concentration；pH 9；298 K；40% MPD, pH 9.0, vapordiffusion, combined with soaking with inhibitor at 1 mM concentration, temperature 298K	Resolution 2.00 Å R-free 0.195
1NM9 Crystal structure of recombinant human salivary amylase mutant W58A Deposited 2003-01-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 16–511（496 aa）	Mutation：W58A Non-standard monomer：Yes (specific site not provided by mmCIF)	HMC 5-HYDROXYMETHYL-CHONDURITOL × 1 GLC alpha-D-glucopyranose × 1 CA CALCIUM ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；323 K；MPD, Calcium chloride, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 323K	Resolution 2.10 Å R-free 0.196
1Q4N Structural studies of Phe256Trp of human salivary alpha-amylase: implications for the role of a conserved water molecule and its associated chain in enzyme activity Deposited 2003-08-04	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 16–511（496 aa）	Mutation：F256W Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 1 CL CHLORIDE ION × 1 TAM TRIS(HYDROXYETHYL)AMINOMETHANE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；MPD, Calcium Chloride, Tris, pH 9.00, VAPOR DIFFUSION, HANGING DROP, temperature 100K	Resolution 2.07 Å R-free 0.206
1XV8 Crystal Structure of Human Salivary Alpha-Amylase Dimer Deposited 2004-10-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 16–511（496 aa） Fragment：HSA Chain B 16–511（496 aa） Fragment：HSA	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 2 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；0.2 M Ca acetate, 0.1 M Na cacodylate (pH 6.5), 18% PEG 8K, VAPOR DIFFUSION, HANGING DROP, temperature 100K	Resolution 3.00 Å R-free 0.271
1Z32 Structure-function relationships in human salivary alpha-amylase: Role of aromatic residues Deposited 2005-03-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 16–511（496 aa）	Mutation：Y151M Non-standard monomer：Yes (specific site not provided by mmCIF)	GLC alpha-D-glucopyranose × 1 AGL 4-amino-4,6-dideoxy-alpha-D-glucopyranose × 1 HMC 5-HYDROXYMETHYL-CHONDURITOL × 1 CA CALCIUM ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；MPD 40%, pH 9.0, VAPOR DIFFUSION, HANGING DROP	Resolution 1.60 Å R-free 0.192
3BLK Role of aromatic residues in starch binding Deposited 2007-12-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 16–511（496 aa）	Mutation：W316A Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 1 CL CHLORIDE ION × 1 HMC 5-HYDROXYMETHYL-CHONDURITOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；298 K；45% MPD, 0.1M Tris.HCl, 10 mM calcium chloride, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.215
3BLP Role of aromatic residues in human salivary alpha-amylase Deposited 2007-12-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain X 16–511（496 aa）	Mutation：W388A Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 1 CL CHLORIDE ION × 1 HMC 5-HYDROXYMETHYL-CHONDURITOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；298 K；45% MPD, 0.1M Tris.HCl, 10 mM calcium chloride, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.60 Å R-free 0.205
3DHP Probing the role of aromatic residues at the secondary saccharide binding sites of human salivary alpha-amylase in substrate hydrolysis and bacterial binding Deposited 2008-06-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 16–511（496 aa）	Mutation：W134A,W203A,Y276A,W284A,W316A,W388A Non-standard monomer：Yes (specific site not provided by mmCIF)	GLC alpha-D-glucopyranose × 1 CA CALCIUM ION × 1 CL CHLORIDE ION × 1 HMC 5-HYDROXYMETHYL-CHONDURITOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions hanging drop；pH 9；298 K；MPD, pH 9.0, hanging drop, temperature 298K	Resolution 1.50 Å R-free 0.186

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

View Construct and Data Evidence

UniProt name	AMYS_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–496； UniProt 17–511

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	1smd
Deposition date deposition_date	1996-01-24
Structure title title	HUMAN SALIVARY AMYLASE
Keywords keywords	HYDROLASE, O-GLYCOSYL, CARBOHYDRATE METABOLISM, HYDROLASE (O-GLYCOSYL); HYDROLASE (O-GLYCOSYL)
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	23.96 Å
Radius of gyration Rg (electron density) rg_electron	22.91 Å
Forward intensity I(0) i0	54714700.00
Molecular weight molecular_weight	55964.0 kDa
Excluded volume excluded_volume	69132 Å³
Envelope volume envelope_volume	77647 Å³
Hydration-shell volume shell_volume	28029 Å³
Envelope diameter envelope_diameter	83.4 Å
Shell Rg shell_rg	30.55 Å
Envelope Rg envelope_rg	23.06 Å
Shape Rg shape_rg	22.90 Å
Total Rg total_rg	23.74 Å
Total atoms total_atoms	3948
Residues n_residues	495
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	80.3 Å
Rg (real space) rg_real	23.90 Å
Rg uncertainty (real space) rg_real_error	0.56 Å
I(0) (real space) i0_real	5.4710e+07
I(0) uncertainty (real space) i0_real_error	7.4150e+05
Rg (reciprocal space) rg_reciprocal	23.92 Å
I(0) (reciprocal space) i0_reciprocal	54720000.0000
Solution quality estimate total_estimate	0.6682
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.9 Å
Skewness Skewness skewness	0.334
Kurtosis Kurtosis kurtosis	-0.209
Angular range angular_range	— – 0.3300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9372000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.796; Stabil: 1.000; Sysdev: 0.101; Positv: 1.000; Valcen: 0.998; Smooth: 0.994

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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	AMYLASE
Molecular weight formula_weight	55955.3 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	4117

QYSSNTQQGRTSIVHLFEWRWVDIALECERYLAPKGFGGVQVSPPNENVAIHNPFRPWWERYQPVSYKLCTRSGNEDEFRNMVTRCNNVGVRIYVDAVINHMCGNAVSAGTSSTCGSYFNPGSRDFPAVPYSGWDFNDGKCKTGSGDIENYNDATQVRDCRLSGLLDLALGKDYVRSKIAEYMNHLIDIGVAGFRIDASKHMWPGDIKAILDKLHNLNSNWFPEGSKPFIYQEVIDLGGEPIKSSDYFGNGRVTEFKYGAKLGTVIRKWNGEKMSYLKNWGEGWGFMPSDRALVFVDNHDNQRGHGAGGASILTFWDARLYKMAVGFMLAHPYGFTRVMSSYRWPRYFENGKDVNDWVGPPNDNGVTKEVTINPDTTCGNDWVCEHRWRQIRNMVNFRNVVDGQPFTNWYDNGSNQVAFGRGNRGFIVFNNDDWTFSLTLQTGLPAGTYCDVISGDKINGNCTGIKIYVSDDGKAHFSISNSAEDPFIAIHAESKL

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 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	169

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1smda1
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	d1smda2
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	d1smda3
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id	1smdA01
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	1smdA02
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 (3)

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Unit-cell length a length_a	53.200 Å
Unit-cell length b length_b	75.400 Å
Unit-cell length c length_c	136.600 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.600 Å
Low-resolution limit resolution_low	6.000 Å
R factor r_factor	—
R_work r_work	0.1840
R_free r_free	—

fit	/app/data/saxs_computation/sm/1smd/1smd.fit
pddf	/app/data/pr_computation/sm/1smd/1smd.pr.out
profile	/app/data/saxs_computation/sm/1smd/1smd.dat

HUMAN SALIVARY AMYLASE

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

AMYLASE

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