1dec

STRUCTURE OF THE RGD PROTEIN DECORSIN: CONSERVED MOTIF AND DISTINCT FUNCTION IN LEECH PROTEINS THAT AFFECT BLOOD CLOTTING

Method: SOLUTION NMR D_max: 25.5 Å Quality: REASONABLE

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

DECORSIN

Macrobdella decora

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 1–39	Not recorded	No other associated polymer	SOLUTION NMR mmCIF provides none of the parsed experimental conditions	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	DECO_MACDE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–39； UniProt 1–39

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1dec
Deposition date deposition_date	1994-05-17
Structure title title	STRUCTURE OF THE RGD PROTEIN DECORSIN: CONSERVED MOTIF AND DISTINCT FUNCTION IN LEECH PROTEINS THAT AFFECT BLOOD CLOTTING
Keywords keywords	BLOOD COAGULATION; BLOOD COAGULATION
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	9.73 Å
Radius of gyration Rg (electron density) rg_electron	10.02 Å
Forward intensity I(0) i0	229832000.00
Molecular weight molecular_weight	109520.0 kDa
Excluded volume excluded_volume	129320 Å³
Envelope volume envelope_volume	10099 Å³
Hydration-shell volume shell_volume	7785 Å³
Envelope diameter envelope_diameter	43.6 Å
Shell Rg shell_rg	16.67 Å
Envelope Rg envelope_rg	12.54 Å
Shape Rg shape_rg	10.06 Å
Total Rg total_rg	10.05 Å
Total atoms total_atoms	14250
Residues n_residues	975
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	25.5 Å
Rg (real space) rg_real	9.25 Å
Rg uncertainty (real space) rg_real_error	0.03 Å
I(0) (real space) i0_real	2.1970e+08
I(0) uncertainty (real space) i0_real_error	1.3430e+06
Rg (reciprocal space) rg_reciprocal	9.81 Å
I(0) (reciprocal space) i0_reciprocal	229800000.0000
Solution quality estimate total_estimate	0.6836
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	0
Primary peak position r_peak_primary	— Å
Skewness Skewness skewness	0.277
Kurtosis Kurtosis kurtosis	-0.514
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	6.2200
Highest regularization parameter α highest_alpha	29310.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.999; Stabil: 0.966; Sysdev: 0.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.000

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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) 1 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1deca_
Class class	g — Small proteins
Fold Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamily	g.3.15 — Leech antihemostatic proteins
Family Family family	g.3.15.2 — Hirudin-like

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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	DECORSIN
Molecular weight formula_weight	4388.9 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	14250

来源生物 organism	Macrobdella decora
通用名 common_name	North American leech
NCBI Class编号 ncbi_taxonomy_id	6405

STRUCTURE OF THE RGD PROTEIN DECORSIN: CONSERVED MOTIF AND DISTINCT FUNCTION IN LEECH PROTEINS THAT AFFECT BLOOD CLOTTING

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

DECORSIN

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) 1 domains

SCOP 2.08 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

fit	/app/data/saxs_computation/de/1dec/1dec.fit
pddf	/app/data/pr_computation/de/1dec/1dec.pr.out
profile	/app/data/saxs_computation/de/1dec/1dec.dat