SAXSdb — 3d3d

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

Lysozyme

Enterobacteria phage lambda

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Monomer	Protein 1 其他Polymer 1	;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-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 SULFATE ION × 3 water × 1	Consistent with protein count
2	Other combination	Monomer	Protein 1 其他Polymer 1	;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-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 1 SULFATE ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LYS_LAMBD
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–154； UniProt 1–154 Author chain B； PDBConstruct 1–154； UniProt 1–154

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	3d3d
Deposition date deposition_date	2008-05-09
Structure title title	Bacteriophage lambda lysozyme complexed with a chitohexasaccharide
Keywords keywords	GLYCOSIDASE, TRANSGLYCOSYLASE, LYSOZYME, PROTEIN-CHITOHEXASSACHARIDE COMPLEX, Antimicrobial, Bacteriolytic enzyme, Hydrolase; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3d3d__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3d3d__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3d3d__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	16.05 Å
Rg (electron density)	14.74 Å
Total Rg	16.07 Å
Atom count	1325
Residues	154
Excluded volume	23307 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3d3d__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3d3d__assembly_2__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Lysozyme
Molecular weight formula_weight	17395.7 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	2679

MVEINNQRKAFLDMLAWSEGTDNGRQKTRNHGYDVIVGGELFTDYSDHPRKLVTLNPKLKSTGAGRYQLLSRWWDAYRKQLGLKDFSPKSQDAVALQQIKERGALPMIDRGDIRQAIDRCSNIWASLPGAGYGQFEHKADSLIAKFKEAGGTVR

Source Source

Source organism organism	Enterobacteria phage lambda
NCBI taxonomy ID ncbi_taxonomy_id	10710
Host organism host_organism	Escherichia coli

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-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	1237.2 kDa
Source method src_method	man
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	39

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3d3da_
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.2.1.4 — Lambda lysozyme

Domain ID domain_id	d3d3db_
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.2.1.4 — Lambda lysozyme

CATH v4.4 (2 domains)

Domain ID domain_id	3d3dA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	530 — Lysozyme
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	3d3dB00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	530 — Lysozyme
Homologous superfamily homologous superfamily	10 —

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Unit-cell length a length_a	52.200 Å
Unit-cell length b length_b	61.081 Å
Unit-cell length c length_c	122.447 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	2.600 Å
Low-resolution limit resolution_low	33.940 Å
R factor r_factor	—
R_work r_work	0.2340
R_free r_free	0.2770

Bacteriophage lambda lysozyme complexed with a chitohexasaccharide

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

Lysozyme

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3d3d__assembly_1__model_1

3d3d__assembly_1__model_1 | I(q)

3d3d__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (2)

Bacteriophage lambda lysozyme complexed with a chitohexasaccharide

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

Lysozyme

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3d3d__assembly_1__model_1

3d3d__assembly_1__model_1 | I(q)

3d3d__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 branched

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (2)