SAXSdb — 1dgn

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

ICEBERG (PROTEASE INHIBITOR)

Homo sapiens

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 2–90	Fragment：RESIDUES 2-90	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 3.8；303 K；Ionic strength (raw mmCIF value) 50 mM SODIUM ACETATE；Pressure AMBIENT NMR measurement conditions：pH 3.8；303 K；Ionic strength (raw mmCIF value) 50 mM SODIUM ACETATE；Pressure AMBIENT NMR measurement conditions：pH 3.8；303 K；Ionic strength (raw mmCIF value) 50 mM SODIUM ACETATE；Pressure AMBIENT NMR sample composition：2MM ICEBERG U-15N; 50MM SODIUM ACETATE-D3; 20 MM DTT-D10; 1MM SODIUM AZIDE 2MM ICEBERG U-15N,13C; 50MM SODIUM ACETATE-D3; 20MM DTT-D10; 1MM SODIUM AZIDE 2MM ICEBERG 15%-13C; 50MM SODIUM ACETATE-D3; 20MM DTT-D10; 1MM SODIUM AZIDE	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	ICBR_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–89； UniProt 2–90

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	1dgn
Deposition date deposition_date	1999-11-24
Structure title title	SOLUTION STRUCTURE OF ICEBERG, AN INHIBITOR OF INTERLEUKIN-1BETA GENERATION
Keywords keywords	ANTIPARALLEL SIX-HELIX BUNDLE, GREEK-KEY, HYDROLASE INHIBITOR; HYDROLASE INHIBITOR
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	12.86 Å
Radius of gyration Rg (electron density) rg_electron	12.28 Å
Forward intensity I(0) i0	586160000.00
Molecular weight molecular_weight	200110.0 kDa
Excluded volume excluded_volume	249250 Å³
Envelope volume envelope_volume	19368 Å³
Hydration-shell volume shell_volume	12154 Å³
Envelope diameter envelope_diameter	43.6 Å
Shell Rg shell_rg	19.41 Å
Envelope Rg envelope_rg	13.69 Å
Shape Rg shape_rg	12.27 Å
Total Rg total_rg	12.47 Å
Total atoms total_atoms	28320
Residues n_residues	1780
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

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

Maximum dimension Dmax dmax	39.3 Å
Rg (real space) rg_real	12.74 Å
Rg uncertainty (real space) rg_real_error	0.29 Å
I(0) (real space) i0_real	5.8620e+08
I(0) uncertainty (real space) i0_real_error	6.3030e+06
Rg (reciprocal space) rg_reciprocal	12.75 Å
I(0) (reciprocal space) i0_reciprocal	586200000.0000
Solution quality estimate total_estimate	0.8622
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	38.3 Å
Skewness Skewness skewness	-0.076
Kurtosis Kurtosis kurtosis	-0.304
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	184200.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.767; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.962; Smooth: 0.943

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1dgna_
Class class	a — All alpha proteins
Fold Fold fold	a.77 — DEATH domain
Superfamily Superfamily superfamily	a.77.1 — DEATH domain
Family Family family	a.77.1.3 — Caspase recruitment domain, CARD

CATH v4.4 (1 domains)

Domain ID domain_id	1dgnA00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	533 — Death Domain, Fas
Homologous superfamily homologous superfamily	10 — Death Domain, Fas

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8. Citations (1)

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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	ICEBERG (PROTEASE INHIBITOR)
Molecular weight formula_weight	10023.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	28320

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

SOLUTION STRUCTURE OF ICEBERG, AN INHIBITOR OF INTERLEUKIN-1BETA GENERATION

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

ICEBERG (PROTEASE INHIBITOR)

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

来源 Source

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/dg/1dgn/1dgn.fit
pddf	/app/data/pr_computation/dg/1dgn/1dgn.pr.out
profile	/app/data/saxs_computation/dg/1dgn/1dgn.dat