SAXSdb — 2ran

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

ANNEXIN V

Rattus norvegicus

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 1–316	Not recorded	CA CALCIUM ION × 7 SO4 SULFATE ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.89 Å

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 2RAN	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1A8A RAT ANNEXIN V COMPLEXED WITH GLYCEROPHOSPHOSERINE Deposited 1998-03-23	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–318（318 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 10 GSE L-ALPHA-GLYCEROPHOSPHORYLSERINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.1；PROTEIN CRYSTALLIZED FROM AMMONIUM SULFATE, 20MM CACL2, 50MM HEPES, PH 8.2; SOAKED IN 20% PEG, 20MM CACL2, 80MM GSE, PH 7.1	Resolution 1.90 Å
1A8B RAT ANNEXIN V COMPLEXED WITH GLYCEROPHOSPHOETHANOLAMINE Deposited 1998-03-23	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–318（318 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 10 GPE L-ALPHA-GLYCEROPHOSPHORYLETHANOLAMINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.1；PROTEIN CRYSTALLIZED FROM AMMONIUM SULFATE, 20MM CACL2, 50MM HEPES, PH 8.2; SOAKED IN 20% PEG, 20MM CACL2, 50MM GPE, PH 7.1	Resolution 1.90 Å
1BC0 RECOMBINANT RAT ANNEXIN V, W185A MUTANT Deposited 1998-05-04	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–318（318 aa）	Mutation：W185A	CA CALCIUM ION × 5 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.2；PROTEIN CRYSTALLIZED FROM AMMONIUM SULFATE, 20MM CACL2, 50MM HEPPS, PH 8.2	Resolution 2.00 Å R-free 0.296
1BC1 RECOMBINANT RAT ANNEXIN V, QUADRUPLE MUTANT (T72K, S144K, S228K, S303K) Deposited 1998-05-04	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–318（318 aa）	Mutation：T72K, S144K, S228K, S303K	CA CALCIUM ION × 5 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.2；PROTEIN CRYSTALLIZED FROM AMMONIUM SULFATE, 20MM CACL2, 50MM HEPPS, PH 8.2	Resolution 2.05 Å R-free 0.254
1BC3 RECOMBINANT RAT ANNEXIN V, TRIPLE MUTANT (T72K, S144K, S228K) Deposited 1998-05-04	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–318（318 aa）	Mutation：T72K, S144K, S228K	CA CALCIUM ION × 5 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.2；PROTEIN CRYSTALLIZED FROM AMMONIUM SULFATE, 20MM CACL2, 50MM HEPPS, PH 8.2	Resolution 1.95 Å R-free 0.211
1BCW RECOMBINANT RAT ANNEXIN V, T72A MUTANT Deposited 1998-05-04	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–318（318 aa）	Mutation：T72A	CA CALCIUM ION × 5 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.2；PROTEIN CRYSTALLIZED FROM AMMONIUM SULFATE, 20MM CACL2, 50MM HEPPS, PH 8.2	Resolution 2.10 Å R-free 0.266
1BCY RECOMBINANT RAT ANNEXIN V, T72K MUTANT Deposited 1998-05-04	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–318（318 aa）	Mutation：T72K	CA CALCIUM ION × 5 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.2；PROTEIN CRYSTALLIZED FROM AMMONIUM SULFATE, 20MM CACL2, 50MM HEPPS, PH 8.2	Resolution 1.95 Å R-free 0.292
1BCZ RECOMBINANT RAT ANNEXIN V, T72S MUTANT Deposited 1998-05-04	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–318（318 aa）	Mutation：T72S	CA CALCIUM ION × 5 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.2；PROTEIN CRYSTALLIZED FROM AMMONIUM SULFATE, 20MM CACL2, 50MM HEPPS, PH 8.2	Resolution 2.20 Å R-free 0.299
1G5N ANNEXIN V COMPLEX WITH HEPARIN OLIGOSACCHARIDES Deposited 2000-11-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–318（318 aa）	Not recorded	CA CALCIUM ION × 9	X-RAY DIFFRACTION X-ray crystallization conditions soaking；pH 8.2；290 K；PEG 4000, calcium chloride, HEPES buffer, pH 8.2, soaking, temperature 290.0K	Resolution 1.90 Å R-free 0.238
1N41 Crystal Structure of Annexin V K27E Mutant Deposited 2002-10-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–319（319 aa）	Mutation：K27E	CA CALCIUM ION × 5 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.2；290 K；ammonium sulfate, CaCl2, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 290K	Resolution 2.10 Å R-free 0.223
1N42 Crystal Structure of Annexin V R149E Mutant Deposited 2002-10-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–319（319 aa）	Mutation：R149E	CA CALCIUM ION × 5 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.2；290 K；ammonium sulfate, CaCl2, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 290K	Resolution 2.10 Å R-free 0.239
1N44 Crystal Structure of Annexin V R23E Mutant Deposited 2002-10-30	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–319（319 aa）	Mutation：R23E	CA CALCIUM ION × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.2；290 K；ammonium sulfate, CaCl2, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 290K	Resolution 3.00 Å R-free 0.241
2H0K Crystal Structure of a Mutant of Rat Annexin A5 Deposited 2006-05-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–318（318 aa）	Mutation：YES	CA CALCIUM ION × 11	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；293 K；PEG 8000, CALCIUM ACETATE, SODIUM CACODYLATE, SODIUM AZIDE, PH 6.4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293.0K, pH 6.40	Resolution 2.76 Å R-free 0.261
2H0K Crystal Structure of a Mutant of Rat Annexin A5 Deposited 2006-05-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–318（318 aa）	Mutation：YES	CA CALCIUM ION × 11	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；293 K；PEG 8000, CALCIUM ACETATE, SODIUM CACODYLATE, SODIUM AZIDE, PH 6.4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293.0K, pH 6.40	Resolution 2.76 Å R-free 0.261
2H0L Crystal Structure of a Mutant of Rat Annexin A5 Deposited 2006-05-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–318（318 aa）	Mutation：YES	CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；PEG 4000, 300MM SODIUM ACETATA, 100MM TRIS, 3MM SODIUM AZIDE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K, pH 8.50	Resolution 2.59 Å R-free 0.278
2H0M Structure of a Mutant of Rat Annexin A5 Deposited 2006-05-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–317（317 aa）	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；PEG 4000 8%, ISOPROPANOL 10%, SODIUM CITRATE 100MM, SODIUM AZIDE 3MM, VAPOR DIFFUSION, HANGING DROP, pH 6.00, temperature 293.0K	Resolution 2.26 Å R-free 0.278
2IE6 Annexin V under 2.0 MPa pressure of xenon Deposited 2006-09-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–318（318 aa）	Not recorded	CA CALCIUM ION × 18 SO4 SULFATE ION × 12 XE XENON × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；annexin V 10mg/ml, Tris HCL 20mM, PH 8, NACL 235MM, (NH4)SO4 1.76M, CACL2 12MM, HEPES 100MM, NAN3 3MM, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.83 Å R-free 0.200
2IE7 Annexin V under 2.0 MPa pressure of nitrous oxide Deposited 2006-09-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1–318（318 aa）	Not recorded	CA CALCIUM ION × 21 SO4 SULFATE ION × 12 N2O NITROUS OXIDE × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；annexin V 10mg/ml, Tris HCL 20mM, PH 8, NACL 235MM, (NH4)SO4 1.76M, CACL2 12MM, HEPES 100MM, NAN3 3MM, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.75 Å R-free 0.203

17 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ANXA5_RAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–316； UniProt 1–316

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	2ran
Deposition date deposition_date	1994-09-01
Structure title title	RAT ANNEXIN V CRYSTAL STRUCTURE: CA2+-INDUCED CONFORMATIONAL CHANGES
Keywords keywords	CALCIUM/PHOSPHOLIPID-BINDING PROTEIN, CALCIUM-PHOSPHOLIPID-BINDING PROTEIN complex; CALCIUM/PHOSPHOLIPID-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	22.66 Å
Radius of gyration Rg (electron density) rg_electron	21.76 Å
Forward intensity I(0) i0	22352400.00
Molecular weight molecular_weight	35828.0 kDa
Excluded volume excluded_volume	44785 Å³
Envelope volume envelope_volume	51981 Å³
Hydration-shell volume shell_volume	20865 Å³
Envelope diameter envelope_diameter	78.2 Å
Shell Rg shell_rg	27.74 Å
Envelope Rg envelope_rg	21.91 Å
Shape Rg shape_rg	21.74 Å
Total Rg total_rg	22.59 Å
Total atoms total_atoms	3077
Residues n_residues	316
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	76.8 Å
Rg (real space) rg_real	22.71 Å
Rg uncertainty (real space) rg_real_error	0.46 Å
I(0) (real space) i0_real	2.2350e+07
I(0) uncertainty (real space) i0_real_error	2.6840e+05
Rg (reciprocal space) rg_reciprocal	22.70 Å
I(0) (reciprocal space) i0_reciprocal	22350000.0000
Solution quality estimate total_estimate	0.8710
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.4 Å
Skewness Skewness skewness	0.460
Kurtosis Kurtosis kurtosis	-0.083
Angular range angular_range	— – 0.3500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5117000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.787; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.981

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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 V
Molecular weight formula_weight	35427.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3185

ALRGTVTDFSGFDGRADAEVLRKAMKGLGTDEDSILNLLTARSNAQRQQIAEEFKTLFGRDLVNDMKSELTGKFEKLIVALMKPSRLYDAYELKHALKGAGTDEKVLTEIIASRTPEELRAIKQAYEEEYGSNLEDDVVGDTSGYYQRMLVVLLQANRDPDTAIDDAQVELDAQALFQAGELKWGTDEEKFITILGTRSVSHLRRVFDKYMTISGFQIEETIDRETSGNLENLLLAVVKSIRSIPAYLAETLYYAMKGAGTDDHTLIRVIVSRSEIDLFNIRKEFRKNFATSLYSMIKGDTSGDYKKALLLLCGGE

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway rat
NCBI Class编号 ncbi_taxonomy_id	10116

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 3 Entity 3 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 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	108

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2rana_
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	2ranA01
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	2ranA02
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	2ranA03
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	2ranA04
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	156.900 Å
Unit-cell length b length_b	156.900 Å
Unit-cell length c length_c	37.030 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	9

Space group space_group	H 3
Space-group number int_tables_number	146
Crystal system crystal_system	—

Resolution resolution	1.890 Å
Low-resolution limit resolution_low	21.320 Å
R factor r_factor	0.2120
R_work r_work	0.2120
R_free r_free	—

fit	/app/data/saxs_computation/ra/2ran/2ran.fit
pddf	/app/data/pr_computation/ra/2ran/2ran.pr.out
profile	/app/data/saxs_computation/ra/2ran/2ran.dat

RAT ANNEXIN V CRYSTAL STRUCTURE: CA2+-INDUCED CONFORMATIONAL CHANGES