SAXSdb — 1b8w

▼

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

PROTEIN (DEFENSIN-LIKE PEPTIDE 1)

OrganismNot specified

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–42	Not recorded	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 3.9；298 K NMR sample composition：3.4MM	Resolution not provided

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	DLP1_ORNAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–42； UniProt 1–42

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	1b8w
Deposition date deposition_date	1999-02-02
Structure title title	DEFENSIN-LIKE PEPTIDE 1
Keywords keywords	TOXIN, PLATYPUS; TOXIN
Experimental Method method	SOLUTION NMR

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	10.19 Å
Radius of gyration Rg (electron density) rg_electron	10.78 Å
Forward intensity I(0) i0	181609000.00
Molecular weight molecular_weight	99213.0 kDa
Excluded volume excluded_volume	118620 Å³
Envelope volume envelope_volume	13689 Å³
Hydration-shell volume shell_volume	9142 Å³
Envelope diameter envelope_diameter	46.8 Å
Shell Rg shell_rg	18.54 Å
Envelope Rg envelope_rg	14.74 Å
Shape Rg shape_rg	10.85 Å
Total Rg total_rg	10.78 Å
Total atoms total_atoms	13360
Residues n_residues	840
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

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	26.8 Å
Rg (real space) rg_real	9.60 Å
Rg uncertainty (real space) rg_real_error	0.03 Å
I(0) (real space) i0_real	1.7390e+08
I(0) uncertainty (real space) i0_real_error	1.1990e+06
Rg (reciprocal space) rg_reciprocal	10.29 Å
I(0) (reciprocal space) i0_reciprocal	181600000.0000
Solution quality estimate total_estimate	0.6875
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	11.5 Å
Skewness Skewness skewness	0.277
Kurtosis Kurtosis kurtosis	-0.413
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	3.5570
Highest regularization parameter α highest_alpha	40270.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.001; Oscil: 0.994; Stabil: 0.985; Sysdev: 0.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (1)

▼

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1b8wa_
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 (1 domains)

Domain ID domain_id	1b8wA00
Class class	2 — Mainly Beta
Architecture architecture	20 — Single Sheet
Topology topology	20 — Anthopleurin-A
Homologous superfamily homologous superfamily	10 — Anthopleurin-A

▶

8. Citations (3)

▶

Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

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

Description description	PROTEIN (DEFENSIN-LIKE PEPTIDE 1)
Molecular weight formula_weight	4968.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	13360

fit	/app/data/saxs_computation/b8/1b8w/1b8w.fit
pddf	/app/data/pr_computation/b8/1b8w/1b8w.pr.out
profile	/app/data/saxs_computation/b8/1b8w/1b8w.dat

DEFENSIN-LIKE PEPTIDE 1

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

PROTEIN (DEFENSIN-LIKE PEPTIDE 1)

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (3)

9. Files and Curves (10)

Files (7)

Curves (3)