SAXSdb — 3blk

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

Alpha-amylase 1

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	Other combination Monomer Protein × 1 其他Polymer 2 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 16–511	Mutation：W316A Non-standard monomer：Yes (specific site not provided by mmCIF)	4-amino-4,6-dideoxy-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose × 2 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

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 3BLK	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 mutation/modification 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 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 mutation/modification 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 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 mutation/modification 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 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 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）	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 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 oligomeric state 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 mutation/modification 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 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 oligomeric state 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
3BLP Role of aromatic residues in human salivary alpha-amylase Deposited 2007-12-11	Different mutation/modification 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	AMY1_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	3blk
Deposition date deposition_date	2007-12-11
Structure title title	Role of aromatic residues in starch binding
Keywords keywords	;TIM Barrel, Greek Key barrel, Calcium, Carbohydrate metabolism, Chloride, Glycoprotein, Glycosidase, Hydrolase, Metal-binding, Pyrrolidone carboxylic acid, Secreted ;; 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	24.05 Å
Radius of gyration Rg (electron density) rg_electron	22.99 Å
Forward intensity I(0) i0	56046600.00
Molecular weight molecular_weight	56644.0 kDa
Excluded volume excluded_volume	69977 Å³
Envelope volume envelope_volume	79175 Å³
Hydration-shell volume shell_volume	28416 Å³
Envelope diameter envelope_diameter	83.9 Å
Shell Rg shell_rg	30.67 Å
Envelope Rg envelope_rg	23.18 Å
Shape Rg shape_rg	22.99 Å
Total Rg total_rg	23.81 Å
Total atoms total_atoms	3993
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	80.0 Å
Rg (real space) rg_real	23.99 Å
Rg uncertainty (real space) rg_real_error	0.49 Å
I(0) (real space) i0_real	5.6050e+07
I(0) uncertainty (real space) i0_real_error	6.9040e+05
Rg (reciprocal space) rg_reciprocal	24.00 Å
I(0) (reciprocal space) i0_reciprocal	56050000.0000
Solution quality estimate total_estimate	0.8752
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.8 Å
Skewness Skewness skewness	0.343
Kurtosis Kurtosis kurtosis	-0.205
Angular range angular_range	— – 0.3300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	11370000.0000
Real-space data points n_real_points	65
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.808; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.952

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Alpha-amylase 1
Molecular weight formula_weight	55840.1 kDa
EC 编号 ec_number	3.2.1.1
Mutation mutation	W316A
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	4181

QYSSNTQQGRTSIVHLFEWRWVDIALECERYLAPKGFGGVQVSPPNENVAIHNPFRPWWERYQPVSYKLCTRSGNEDEFRNMVTRCNNVGVRIYVDAVINHMCGNAVSAGTSSTCGSYFNPGSRDFPAVPYSGWDFNDGKCKTGSGDIENYNDATQVRDCRLSGLLDLALGKDYVRSKIAEYMNHLIDIGVAGFRIDASKHMWPGDIKAILDKLHNLNSNWFPEGSKPFIYQEVIDLGGEPIKSSDYFGNGRVTEFKYGAKLGTVIRKWNGEKMSYLKNWGEGWGFMPSDRALVFVDNHDNQRGHGAGGASILTFADARLYKMAVGFMLAHPYGFTRVMSSYRWPRYFENGKDVNDWVGPPNDNGVTKEVTINPDTTCGNDWVCEHRWRQIRNMVNFRNVVDGQPFTNWYDNGSNQVAFGRGNRGFIVFNNDDWTFSLTLQTGLPAGTYCDVISGDKINGNCTGIKIYVSDDGKAHFSISNSAEDPFIAIHAESKL

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 branched

Description description	4-amino-4,6-dideoxy-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
Molecular weight formula_weight	325.3 kDa
Source method src_method	man
Copy count entity_count	2

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 non-polymer

Description description	5-HYDROXYMETHYL-CHONDURITOL
Molecular weight formula_weight	176.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	188

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3blka1
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	d3blka2
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

CATH v4.4 (2 domains)

Domain ID domain_id	3blkA01
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	3blkA02
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	52.282 Å
Unit-cell length b length_b	75.046 Å
Unit-cell length c length_c	135.013 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	2.000 Å
Low-resolution limit resolution_low	36.160 Å
R factor r_factor	0.1776
R_work r_work	0.1757
R_free r_free	0.2147

fit	/app/data/saxs_computation/bl/3blk/3blk.fit
pddf	/app/data/pr_computation/bl/3blk/3blk.pr.out
profile	/app/data/saxs_computation/bl/3blk/3blk.dat

Role of aromatic residues in starch binding