SAXSdb — 1c8q

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

ALPHA-AMYLASE

Homo sapiens

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 16–511	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

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 1C8Q	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1JXJ Role of mobile loop in the mechanism of human salivary amylase Deposited 2001-09-07	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 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 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 construct 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 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 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
1SMD HUMAN SALIVARY AMYLASE Deposited 1996-01-24	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 17–511（495 aa）	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 conditions	Resolution 1.60 Å
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 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 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 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 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 1–496； UniProt 16–511

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	1c8q
Deposition date deposition_date	2000-06-08
Structure title title	STRUCTURE SOLUTION AND REFINEMENT OF THE RECOMBINANT HUMAN SALIVARY AMYLASE
Keywords keywords	beta barrel, recombinant amylase, human saliva, 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	23.87 Å
Radius of gyration Rg (electron density) rg_electron	22.81 Å
Forward intensity I(0) i0	54706200.00
Molecular weight molecular_weight	55964.0 kDa
Excluded volume excluded_volume	69132 Å³
Envelope volume envelope_volume	77081 Å³
Hydration-shell volume shell_volume	27933 Å³
Envelope diameter envelope_diameter	83.4 Å
Shell Rg shell_rg	30.44 Å
Envelope Rg envelope_rg	22.97 Å
Shape Rg shape_rg	22.80 Å
Total Rg total_rg	23.65 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	83.1 Å
Rg (real space) rg_real	23.81 Å
Rg uncertainty (real space) rg_real_error	0.70 Å
I(0) (real space) i0_real	5.4710e+07
I(0) uncertainty (real space) i0_real_error	7.3710e+05
Rg (reciprocal space) rg_reciprocal	23.82 Å
I(0) (reciprocal space) i0_reciprocal	54710000.0000
Solution quality estimate total_estimate	0.6099
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	29.9 Å
Skewness Skewness skewness	0.333
Kurtosis Kurtosis kurtosis	-0.212
Angular range angular_range	— – 0.3350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	10560000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.701; Stabil: 0.993; Sysdev: 0.286; Positv: 1.000; Valcen: 0.985; Smooth: 0.000

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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	ALPHA-AMYLASE
Molecular weight formula_weight	55955.3 kDa
EC 编号 ec_number	3.2.1.1
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4215

QYSSNTQQGRTSIVHLFEWRWVDIALECERYLAPKGFGGVQVSPPNENVAIHNPFRPWWERYQPVSYKLCTRSGNEDEFRNMVTRCNNVGVRIYVDAVINHMCGNAVSAGTSSTCGSYFNPGSRDFPAVPYSGWDFNDGKCKTGSGDIENYNDATQVRDCRLSGLLDLALGKDYVRSKIAEYMNHLIDIGVAGFRIDASKHMWPGDIKAILDKLHNLNSNWFPEGSKPFIYQEVIDLGGEPIKSSDYFGNGRVTEFKYGAKLGTVIRKWNGEKMSYLKNWGEGWGFMPSDRALVFVDNHDNQRGHGAGGASILTFWDARLYKMAVGFMLAHPYGFTRVMSSYRWPRYFENGKDVNDWVGPPNDNGVTKEVTINPDTTCGNDWVCEHRWRQIRNMVNFRNVVDGQPFTNWYDNGSNQVAFGRGNRGFIVFNNDDWTFSLTLQTGLPAGTYCDVISGDKINGNCTGIKIYVSDDGKAHFSISNSAEDPFIAIHAESKL

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Spodoptera frugiperda

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	267

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1c8qa1
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	d1c8qa2
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

CATH v4.4 (2 domains)

Domain ID domain_id	1c8qA01
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	1c8qA02
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	52.707 Å
Unit-cell length b length_b	74.768 Å
Unit-cell length c length_c	133.337 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	2.300 Å
Low-resolution limit resolution_low	9.990 Å
R factor r_factor	—
R_work r_work	0.1730
R_free r_free	0.2160

fit	/app/data/saxs_computation/c8/1c8q/1c8q.fit
pddf	/app/data/pr_computation/c8/1c8q/1c8q.pr.out
profile	/app/data/saxs_computation/c8/1c8q/1c8q.dat

STRUCTURE SOLUTION AND REFINEMENT OF THE RECOMBINANT HUMAN SALIVARY AMYLASE

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

ALPHA-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

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