1fd4

HUMAN BETA-DEFENSIN 2

Method: X-RAY DIFFRACTION

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

BETA-DEFENSIN 2

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 1 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 1 water × 2	Consistent with protein count
4	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count
5	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 2 water × 2	Consistent with protein count
6	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count
7	Protein homooligomer	Homooligomer	Protein 2	SULFATE ION × 1 water × 2	Consistent with protein count
8	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	BD02_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–41； UniProt 24–64 Author chain B； PDBConstruct 1–41； UniProt 24–64 Author chain C； PDBConstruct 1–41； UniProt 24–64 Author chain D； PDBConstruct 1–41； UniProt 24–64 Author chain E； PDBConstruct 1–41； UniProt 24–64 Author chain F； PDBConstruct 1–41； UniProt 24–64 Author chain G； PDBConstruct 1–41； UniProt 24–64 Author chain H； PDBConstruct 1–41； UniProt 24–64 Author chain I； PDBConstruct 1–41； UniProt 24–64 Author chain J； PDBConstruct 1–41； UniProt 24–64 Author chain K； PDBConstruct 1–41； UniProt 24–64 Author chain L； PDBConstruct 1–41； UniProt 24–64 Author chain M； PDBConstruct 1–41； UniProt 24–64 Author chain N； PDBConstruct 1–41； UniProt 24–64 Author chain O； PDBConstruct 1–41； UniProt 24–64 Author chain P； PDBConstruct 1–41； UniProt 24–64

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	1fd4
Deposition date deposition_date	2000-07-19
Structure title title	HUMAN BETA-DEFENSIN 2
Keywords keywords	DEFENSIN, HUMAN BETA-DEFENSIN 2, BETA-DEFENSIN, ANTIMICROBIAL PEPTIDE; ANTIMICROBIAL PEPTIDE
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.

1fd4__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1fd4__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1fd4__assembly_4__model_1 | P(r) · Pending

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

Rg（Guinier）	12.28 Å
Rg (electron density)	11.25 Å
Total Rg	12.63 Å
Atom count	598
Residues	82
Excluded volume	10866 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1fd4__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1fd4__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1fd4__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1fd4__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`1fd4__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`1fd4__assembly_6__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`1fd4__assembly_7__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`1fd4__assembly_8__model_1`	dimeric （2）	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 (3)

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6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

Domain ID domain_id	d1fd4a_
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	d1fd4b_
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	d1fd4c_
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	d1fd4d_
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	d1fd4e_
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	d1fd4f_
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	d1fd4g_
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	d1fd4h_
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	d1fd4i_
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	d1fd4j_
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	d1fd4k_
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	d1fd4l_
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	d1fd4m_
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	d1fd4n_
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	d1fd4o_
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	d1fd4p_
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

CATH v4.4 (16 domains)

Domain ID domain_id	1fd4A00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	360 — Antimicrobial Peptide, Beta-defensin 2; Chain A
Homologous superfamily homologous superfamily	10 — Antimicrobial Peptide, Beta-defensin 2; Chain A

Domain ID domain_id	1fd4B00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	360 — Antimicrobial Peptide, Beta-defensin 2; Chain A
Homologous superfamily homologous superfamily	10 — Antimicrobial Peptide, Beta-defensin 2; Chain A

Domain ID domain_id	1fd4C00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	360 — Antimicrobial Peptide, Beta-defensin 2; Chain A
Homologous superfamily homologous superfamily	10 — Antimicrobial Peptide, Beta-defensin 2; Chain A

Domain ID domain_id	1fd4D00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	360 — Antimicrobial Peptide, Beta-defensin 2; Chain A
Homologous superfamily homologous superfamily	10 — Antimicrobial Peptide, Beta-defensin 2; Chain A

Domain ID domain_id	1fd4E00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	360 — Antimicrobial Peptide, Beta-defensin 2; Chain A
Homologous superfamily homologous superfamily	10 — Antimicrobial Peptide, Beta-defensin 2; Chain A

Domain ID domain_id	1fd4F00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	360 — Antimicrobial Peptide, Beta-defensin 2; Chain A
Homologous superfamily homologous superfamily	10 — Antimicrobial Peptide, Beta-defensin 2; Chain A

Domain ID domain_id	1fd4G00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	360 — Antimicrobial Peptide, Beta-defensin 2; Chain A
Homologous superfamily homologous superfamily	10 — Antimicrobial Peptide, Beta-defensin 2; Chain A

Domain ID domain_id	1fd4H00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	360 — Antimicrobial Peptide, Beta-defensin 2; Chain A
Homologous superfamily homologous superfamily	10 — Antimicrobial Peptide, Beta-defensin 2; Chain A

Domain ID domain_id	1fd4I00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	360 — Antimicrobial Peptide, Beta-defensin 2; Chain A
Homologous superfamily homologous superfamily	10 — Antimicrobial Peptide, Beta-defensin 2; Chain A

Domain ID domain_id	1fd4J00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	360 — Antimicrobial Peptide, Beta-defensin 2; Chain A
Homologous superfamily homologous superfamily	10 — Antimicrobial Peptide, Beta-defensin 2; Chain A

Domain ID domain_id	1fd4K00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	360 — Antimicrobial Peptide, Beta-defensin 2; Chain A
Homologous superfamily homologous superfamily	10 — Antimicrobial Peptide, Beta-defensin 2; Chain A

Domain ID domain_id	1fd4L00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	360 — Antimicrobial Peptide, Beta-defensin 2; Chain A
Homologous superfamily homologous superfamily	10 — Antimicrobial Peptide, Beta-defensin 2; Chain A

Domain ID domain_id	1fd4M00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	360 — Antimicrobial Peptide, Beta-defensin 2; Chain A
Homologous superfamily homologous superfamily	10 — Antimicrobial Peptide, Beta-defensin 2; Chain A

Domain ID domain_id	1fd4N00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	360 — Antimicrobial Peptide, Beta-defensin 2; Chain A
Homologous superfamily homologous superfamily	10 — Antimicrobial Peptide, Beta-defensin 2; Chain A

Domain ID domain_id	1fd4O00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	360 — Antimicrobial Peptide, Beta-defensin 2; Chain A
Homologous superfamily homologous superfamily	10 — Antimicrobial Peptide, Beta-defensin 2; Chain A

Domain ID domain_id	1fd4P00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	360 — Antimicrobial Peptide, Beta-defensin 2; Chain A
Homologous superfamily homologous superfamily	10 — Antimicrobial Peptide, Beta-defensin 2; Chain A

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Unit-cell length a length_a	54.525 Å
Unit-cell length b length_b	79.950 Å
Unit-cell length c length_c	74.271 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	105.30 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	32

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.700 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	0.1876
R_work r_work	0.1878
R_free r_free	0.2639

Description description	BETA-DEFENSIN 2
Molecular weight formula_weight	4342.3 kDa
Source method src_method	syn
Copy count entity_count	16

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P
Atom count atom_count	5818

HUMAN BETA-DEFENSIN 2

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

BETA-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

1fd4__assembly_4__model_1

1fd4__assembly_4__model_1 | I(q)

1fd4__assembly_4__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

CATH v4.4 (16 domains)

7. Citations (1)

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	5

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	806

HUMAN BETA-DEFENSIN 2

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

BETA-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

1fd4__assembly_4__model_1

1fd4__assembly_4__model_1 | I(q)

1fd4__assembly_4__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (16 domains)

CATH v4.4 (16 domains)

7. Citations (1)