SAXSdb — 1lzs

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

HUMAN LYSOZYME

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 19–148	Not recorded	;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.60 Å
2	Other combination Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 19–148	Not recorded	;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 NA SODIUM 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 1LZS	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1D6P HUMAN LYSOZYME L63 MUTANT LABELLED WITH 2',3'-EPOXYPROPYL N,N'-DIACETYLCHITOBIOSE Deposited 1999-10-15	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 19–148（130 aa）	Mutation：Y63L	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；298 K；5M NH4NO3 IN 10 MM NAOAC(PH 4.5), VAPOR DIFFUSION, SITTING DROP, temperature 298.0K	Resolution 2.23 Å R-free 0.216
1D6Q HUMAN LYSOZYME E102 MUTANT LABELLED WITH 2',3'-EPOXYPROPYL GLYCOSIDE OF N-ACETYLLACTOSAMINE Deposited 1999-10-15	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 19–148（130 aa）	Mutation：D102E	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；298 K；5M NH4NO3 IN 10 MM NAOAC (PH4.5), VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 1.96 Å R-free 0.248
1LMT STRUCTURE OF A CONFORMATIONALLY CONSTRAINED ARG-GLY-ASP SEQUENCE INSERTED INTO HUMAN LYSOZYME Deposited 1995-01-13	Different construct Different ligand/ion	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 19–142（124 aa）	Not recorded	CL CHLORIDE ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.60 Å
1LZR STRUCTURAL CHANGES OF THE ACTIVE SITE CLEFT AND DIFFERENT SACCHARIDE BINDING MODES IN HUMAN LYSOZYME CO-CRYSTALLIZED WITH HEXA-N-ACETYL-CHITOHEXAOSE AT PH 4.0 Deposited 1994-09-14	Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 19–148（130 aa）	Not recorded	CL CHLORIDE ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.50 Å
1RE2 HUMAN LYSOZYME LABELLED WITH TWO 2',3'-EPOXYPROPYL BETA-GLYCOSIDE OF N-ACETYLLACTOSAMINE Deposited 1998-11-05	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 19–148（130 aa）	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；pH 4.5	Resolution 2.30 Å R-free 0.247
1REM HUMAN LYSOZYME WITH MAN-B1,4-GLCNAC COVALENTLY ATTACHED TO ASP53 Deposited 1998-01-14	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 19–148（130 aa）	Not recorded	NO3 NITRATE ION × 1 PGR R-1,2-PROPANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；5M AMMONIUM NITRATE IN 20MM SODIUM ACETATE (PH 4.5)	Resolution 2.10 Å R-free 0.248
1REY HUMAN LYSOZYME-N,N'-DIACETYLCHITOBIOSE COMPLEX Deposited 1996-08-21	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 19–148（130 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；pH 4.5	Resolution 1.70 Å R-free 0.224
1REZ HUMAN LYSOZYME-N-ACETYLLACTOSAMINE COMPLEX Deposited 1996-08-21	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 19–148（130 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.5；pH 4.5	Resolution 1.70 Å R-free 0.215
1UBZ Crystal structure of Glu102-mutant human lysozyme doubly labeled with 2',3'-epoxypropyl beta-glycoside of N-acetyllactosamine Deposited 2003-04-07	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 19–148（130 aa）	Mutation：D102E	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；298 K；sodium acetate, sodium nitrate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K	Resolution 2.00 Å R-free 0.266
1W08 STRUCTURE OF T70N HUMAN LYSOZYME Deposited 2004-06-02	Different construct 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 19–148（130 aa） Fragment：RESIDUES 19-148	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；HANGING DROP METHOD AT 293K. DROPLET RESERVOIR SOLUTION MIXED 1:1 WITH 10 MG/ML PROTEIN, 10 MM HEPES BUFFER PH 7.5, 0.4 M LICL. RESERVOIR 2.5 M NACL, 20 MM NAOAC PH 4.5.	Resolution 2.50 Å R-free 0.268
207L MUTANT HUMAN LYSOZYME C77A Deposited 1996-03-26	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 19–148（130 aa）	Mutation：C77A	SC2 N-ACETYL-L-CYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6.0	Resolution 1.80 Å
208L MUTANT HUMAN LYSOZYME C77A Deposited 1996-03-26	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 19–148（130 aa）	Mutation：C77A	CYS CYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；pH 6.0	Resolution 2.20 Å

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

View Construct and Data Evidence

UniProt name	LYC_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–130； UniProt 19–148 Author chain B； PDBConstruct 1–130； UniProt 19–148

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	1lzs
Deposition date deposition_date	1994-09-14
Structure title title	STRUCTURAL CHANGES OF THE ACTIVE SITE CLEFT AND DIFFERENT SACCHARIDE BINDING MODES IN HUMAN LYSOZYME CO-CRYSTALLIZED WITH HEXA-N-ACETYL-CHITOHEXAOSE AT PH 4.0
Keywords keywords	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	22.79 Å
Radius of gyration Rg (electron density) rg_electron	22.24 Å
Forward intensity I(0) i0	19663800.00
Molecular weight molecular_weight	31557.0 kDa
Excluded volume excluded_volume	38587 Å³
Envelope volume envelope_volume	45347 Å³
Hydration-shell volume shell_volume	18155 Å³
Envelope diameter envelope_diameter	75.3 Å
Shell Rg shell_rg	27.49 Å
Envelope Rg envelope_rg	22.39 Å
Shape Rg shape_rg	22.21 Å
Total Rg total_rg	22.95 Å
Total atoms total_atoms	2203
Residues n_residues	260
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	74.6 Å
Rg (real space) rg_real	22.94 Å
Rg uncertainty (real space) rg_real_error	0.52 Å
I(0) (real space) i0_real	1.9660e+07
I(0) uncertainty (real space) i0_real_error	2.3480e+05
Rg (reciprocal space) rg_reciprocal	22.91 Å
I(0) (reciprocal space) i0_reciprocal	19660000.0000
Solution quality estimate total_estimate	0.8654
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.5 Å
Skewness Skewness skewness	0.473
Kurtosis Kurtosis kurtosis	-0.472
Angular range angular_range	— – 0.3500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	4318000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.798; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.873; Smooth: 0.978

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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	HUMAN LYSOZYME
Molecular weight formula_weight	14720.7 kDa
EC 编号 ec_number	3.2.1.17
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2474

KVFERCELARTLKRLGMDGYRGISLANWMCLAKWESGYNTRATNYNAGDRSTDYGIFQINSRYWCNDGKTPGAVNACHLSCSALLQDNIADAVACAKRVVRDPQGIRAWVAWRNRCQNRDVRQYVQGCGV

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606

Entity 2 Entity 2 branched

Description description	;2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	830.8 kDa
Source method src_method	man
Copy count entity_count	2

Entity 3 Entity 3 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	271

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1lzsa_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.2 — Lysozyme-like
Superfamily Superfamily superfamily	d.2.1 — Lysozyme-like
Family Family family	d.2.1.2 — C-type lysozyme

Domain ID domain_id	d1lzsb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.2 — Lysozyme-like
Superfamily Superfamily superfamily	d.2.1 — Lysozyme-like
Family Family family	d.2.1.2 — C-type lysozyme

CATH v4.4 (2 domains)

Domain ID domain_id	1lzsA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	530 — Lysozyme
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	1lzsB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	530 — Lysozyme
Homologous superfamily homologous superfamily	10 —

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8. Citations (1)

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Unit-cell length a length_a	46.990 Å
Unit-cell length b length_b	162.250 Å
Unit-cell length c length_c	32.520 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	1.600 Å
Low-resolution limit resolution_low	6.000 Å
R factor r_factor	0.1700
R_work r_work	—
R_free r_free	—

fit	/app/data/saxs_computation/lz/1lzs/1lzs.fit
pddf	/app/data/pr_computation/lz/1lzs/1lzs.pr.out
profile	/app/data/saxs_computation/lz/1lzs/1lzs.dat

STRUCTURAL CHANGES OF THE ACTIVE SITE CLEFT AND DIFFERENT SACCHARIDE BINDING MODES IN HUMAN LYSOZYME CO-CRYSTALLIZED WITH HEXA-N-ACETYL-CHITOHEXAOSE AT PH 4.0