SAXSdb — 1zmk

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

Neutrophil defensin 2

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	CHLORIDE ION × 2 GLYCEROL × 1 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 8	CHLORIDE ION × 8 GLYCEROL × 4 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DEF3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–29； UniProt 66–94 Author chain B； PDBConstruct 1–29； UniProt 66–94

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	1zmk
Deposition date deposition_date	2005-05-10
Structure title title	Crystal structure of human alpha-defensin-2 (variant Gly16-> D-ALA), P 42 21 2 space group
Keywords keywords	alpha-defensin, antimicrobial, D-amino acid substitutions, ANTIMICROBIAL PROTEIN; ANTIMICROBIAL PROTEIN
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.

1zmk__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1zmk__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1zmk__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	20.34 Å
Rg (electron density)	19.48 Å
Total Rg	20.27 Å
Atom count	1902
Residues	224
Excluded volume	34033 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1zmk__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1zmk__assembly_2__model_1`	octameric （8）	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	Neutrophil defensin 2
Molecular weight formula_weight	3395.1 kDa
Mutation mutation	G16(DAL)
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	559

CYCRIPACIAGERRYATCIYQGRLWAFCC

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 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	75

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6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1zmka_
Class class	g — Small proteins
Fold Fold fold	g.9 — Defensin-like
Superfamily Superfamily superfamily	g.9.1 — Defensin-like
Family Family family	g.9.1.1 — Defensin

Domain ID domain_id	d1zmkb_
Class class	g — Small proteins
Fold Fold fold	g.9 — Defensin-like
Superfamily Superfamily superfamily	g.9.1 — Defensin-like
Family Family family	g.9.1.1 — Defensin

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Unit-cell length a length_a	47.148 Å
Unit-cell length b length_b	47.148 Å
Unit-cell length c length_c	50.643 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	16

Resolution resolution	1.300 Å
Low-resolution limit resolution_low	19.470 Å
R factor r_factor	0.1612
R_work r_work	0.1603
R_free r_free	0.1768

Crystal structure of human alpha-defensin-2 (variant Gly16-> D-ALA), P 42 21 2 space group

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

Neutrophil defensin 2

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

1zmk__assembly_2__model_1

1zmk__assembly_2__model_1 | I(q)

1zmk__assembly_2__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

7. Citations (1)

Space group space_group	P 42 21 2
Space-group number int_tables_number	94
Crystal system crystal_system	—

Crystal structure of human alpha-defensin-2 (variant Gly16-> D-ALA), P 42 21 2 space group

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

Neutrophil defensin 2

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

1zmk__assembly_2__model_1

1zmk__assembly_2__model_1 | I(q)

1zmk__assembly_2__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

7. Citations (1)