SAXSdb — 1zmi

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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	GLYCEROL × 4 SULFATE ION × 3 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 8	GLYCEROL × 8 SULFATE ION × 6 water × 8	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 4	GLYCEROL × 4 SULFATE ION × 3 water × 4	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 4	GLYCEROL × 4 SULFATE ION × 3 water × 4	Consistent with protein count
6	Protein homooligomer	Homooligomer	Protein 4	GLYCEROL × 4 SULFATE ION × 3 water × 4	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 Author chain C； PDBConstruct 1–29； UniProt 66–94 Author chain D； 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	1zmi
Deposition date deposition_date	2005-05-10
Structure title title	Crystal structure of human alpha_defensin-2 (variant GLY16->D-ALA), P 32 2 1 space group )
Keywords keywords	ALPHA-DEFENSIN, ANTIMICROBIAL, D-AMINO ACID SUBSTITUTION, 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.

1zmi__assembly_2__model_1

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

Download this curve (.dat)

1zmi__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1zmi__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	12.04 Å
Rg (electron density)	10.89 Å
Total Rg	12.26 Å
Atom count	468
Residues	56
Excluded volume	8357 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1zmi__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1zmi__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1zmi__assembly_3__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1zmi__assembly_4__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`1zmi__assembly_5__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`1zmi__assembly_6__model_1`	tetrameric （4）	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	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	1099

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	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	4

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	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	122

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1zmia_
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	d1zmib_
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	d1zmic_
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	d1zmid_
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	71.685 Å
Unit-cell length b length_b	71.685 Å
Unit-cell length c length_c	54.882 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	—

Resolution resolution	1.150 Å
Low-resolution limit resolution_low	12.000 Å
R factor r_factor	0.1688
R_work r_work	0.1681
R_free r_free	0.1820

Crystal structure of human alpha_defensin-2 (variant GLY16->D-ALA), P 32 2 1 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

1zmi__assembly_2__model_1

1zmi__assembly_2__model_1 | I(q)

1zmi__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) 4 domains

SCOP 2.08 (4 domains)

7. Citations (1)

Crystal structure of human alpha_defensin-2 (variant GLY16->D-ALA), P 32 2 1 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

1zmi__assembly_2__model_1

1zmi__assembly_2__model_1 | I(q)

1zmi__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) 4 domains

SCOP 2.08 (4 domains)

7. Citations (1)