SAXSdb — 1yj0

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

Annexin A5

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 2–321	Not recorded	SO4 SULFATE ION × 8 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 8；298 K；Ammonium Sulfate, zinc chloride, HEPES, pH 8.0, VAPOR DIFFUSION, temperature 298K	Resolution 2.95 Å R-free 0.286
2	Protein homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 2–321	Not recorded	SO4 SULFATE ION × 24 ZN ZINC ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 8；298 K；Ammonium Sulfate, zinc chloride, HEPES, pH 8.0, VAPOR DIFFUSION, temperature 298K	Resolution 2.95 Å R-free 0.286

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.

Other PDB	Difference from Current Entry 1YJ0	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1ALA STRUCTURE OF CHICKEN ANNEXIN V AT 2.25-ANGSTROMS RESOLUTION Deposited 1993-01-14	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–321（321 aa）	Not recorded	CA CALCIUM ION × 3	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.25 Å
1YII Crystal Structures of Chicken Annexin V in Complex with Ca2+ Deposited 2005-01-11	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–321（320 aa）	Not recorded	SO4 SULFATE ION × 3 CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 8；298 K；Ammonium Sulfate, calcium chloride, HEPES, pH 8.0, VAPOR DIFFUSION, temperature 298K	Resolution 1.42 Å R-free 0.210

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ANXA5_CHICK
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–320； UniProt 2–321

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	1yj0
Deposition date deposition_date	2005-01-11
Structure title title	Crystal Structures of Chicken Annexin V in Complex with Zn2+
Keywords keywords	Annexin; membrane binding; matrix vessicle, PROTEIN AND METAL BINDING PROTEIN; PROTEIN AND METAL BINDING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	22.60 Å
Radius of gyration Rg (electron density) rg_electron	21.56 Å
Forward intensity I(0) i0	25015500.00
Molecular weight molecular_weight	36630.0 kDa
Excluded volume excluded_volume	45303 Å³
Envelope volume envelope_volume	54359 Å³
Hydration-shell volume shell_volume	21649 Å³
Envelope diameter envelope_diameter	79.7 Å
Shell Rg shell_rg	27.73 Å
Envelope Rg envelope_rg	21.80 Å
Shape Rg shape_rg	21.53 Å
Total Rg total_rg	22.45 Å
Total atoms total_atoms	2552
Residues n_residues	317
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	77.5 Å
Rg (real space) rg_real	22.61 Å
Rg uncertainty (real space) rg_real_error	0.51 Å
I(0) (real space) i0_real	2.5020e+07
I(0) uncertainty (real space) i0_real_error	3.4320e+05
Rg (reciprocal space) rg_reciprocal	22.61 Å
I(0) (reciprocal space) i0_reciprocal	25020000.0000
Solution quality estimate total_estimate	0.8678
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.8 Å
Skewness Skewness skewness	0.425
Kurtosis Kurtosis kurtosis	-0.102
Angular range angular_range	— – 0.3500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6518000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.773; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.974

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Annexin A5
Molecular weight formula_weight	36117.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2616

AKYTRGTVTAFSPFDARADAEALRKAMKGMGTDEETILKILTSRNNAQRQEIASAFKTLFGRDLVDDLKSELTGKFETLMVSLMRPARIFDAHALKHAIKGAGTNEKVLTEILASRTPAEVQNIKQVYMQEYEANLEDKITGETSGHFQRLLVVLLQANRDPDGRVDEALVEKDAQVLFRAGELKWGTDEETFITILGTRSVSHLRRVFDKYMTISGFQIEETIDRETSGDLEKLLLAVVKCIRSVPAYFAETLYYSMKGAGTDDDTLIRVMVSRSEIDLLDIRHEFRKNFAKSLYQMIQKDTSGDYRKALLLLCGGDDE

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	64

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1yj0a_
Class class	a — All alpha proteins
Fold Fold fold	a.65 — Annexin
Superfamily Superfamily superfamily	a.65.1 — Annexin
Family Family family	a.65.1.1 — Annexin

CATH v4.4 (4 domains)

Domain ID domain_id	1yj0A01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	220 — Annexin V; domain 1
Homologous superfamily homologous superfamily	10 — Annexin

Domain ID domain_id	1yj0A02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	220 — Annexin V; domain 1
Homologous superfamily homologous superfamily	10 — Annexin

Domain ID domain_id	1yj0A03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	220 — Annexin V; domain 1
Homologous superfamily homologous superfamily	10 — Annexin

Domain ID domain_id	1yj0A04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	220 — Annexin V; domain 1
Homologous superfamily homologous superfamily	10 — Annexin

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8. Citations (1)

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Unit-cell length a length_a	106.593 Å
Unit-cell length b length_b	106.593 Å
Unit-cell length c length_c	106.593 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	12

Space group space_group	P 21 3
Space-group number int_tables_number	198
Crystal system crystal_system	—

Resolution resolution	2.950 Å
Low-resolution limit resolution_low	43.520 Å
R factor r_factor	0.2111
R_work r_work	0.2110
R_free r_free	0.2860

fit	/app/data/saxs_computation/yj/1yj0/1yj0.fit
pddf	/app/data/pr_computation/yj/1yj0/1yj0.pr.out
profile	/app/data/saxs_computation/yj/1yj0/1yj0.dat

Crystal Structures of Chicken Annexin V in Complex with Zn2+

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

Annexin A5

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

Refinement Refinement

Diffraction experiment Diffraction