SAXSdb — 2h0k

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

Annexin A5

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 1–318	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–318	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

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 2H0K	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 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 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 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 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 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 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 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 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 mutation/modification 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
2H0L Crystal Structure of a Mutant of Rat Annexin A5 Deposited 2006-05-15	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 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 mutation/modification 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 mutation/modification 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
2RAN RAT ANNEXIN V CRYSTAL STRUCTURE: CA2+-INDUCED CONFORMATIONAL CHANGES Deposited 1994-09-01	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 1–316（316 aa）	Not recorded	CA CALCIUM ION × 7 SO4 SULFATE ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.89 Å

17 other PDB entries and 17 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 1–318； UniProt 1–318 Author chain B； PDBConstruct 1–318； UniProt 1–318

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	2h0k
Deposition date deposition_date	2006-05-15
Structure title title	Crystal Structure of a Mutant of Rat Annexin A5
Keywords keywords	PHOSPHOLIPID MEMBRANE BINDING PROTEINS, BLOOD CLOTTING; BLOOD CLOTTING
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	33.69 Å
Radius of gyration Rg (electron density) rg_electron	33.29 Å
Forward intensity I(0) i0	81685200.00
Molecular weight molecular_weight	71862.0 kDa
Excluded volume excluded_volume	89776 Å³
Envelope volume envelope_volume	116740 Å³
Hydration-shell volume shell_volume	30747 Å³
Envelope diameter envelope_diameter	107.1 Å
Shell Rg shell_rg	37.92 Å
Envelope Rg envelope_rg	33.14 Å
Shape Rg shape_rg	33.30 Å
Total Rg total_rg	33.61 Å
Total atoms total_atoms	5018
Residues n_residues	636
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	109.8 Å
Rg (real space) rg_real	33.84 Å
Rg uncertainty (real space) rg_real_error	0.96 Å
I(0) (real space) i0_real	8.1690e+07
I(0) uncertainty (real space) i0_real_error	1.4000e+06
Rg (reciprocal space) rg_reciprocal	33.75 Å
I(0) (reciprocal space) i0_reciprocal	81680000.0000
Solution quality estimate total_estimate	0.7909
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	30.4 Å
Skewness Skewness skewness	0.371
Kurtosis Kurtosis kurtosis	-0.703
Angular range angular_range	— – 0.2350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	11400000.0000
Real-space data points n_real_points	48
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.837; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.766; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Annexin A5
Molecular weight formula_weight	35584.8 kDa
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5185

ALRGTVTDFSGFDGEADAEVLEKAMEGLGTDEDSILNLLTARSNAQRQQIAEEFETLFGRDLVNDMKSELTGKFEKLIVALMKPSRLYDAYELKHALKGAGTDEKVLTEIIASRTPEELRAIKQAYEEEYGSNLEDDVVGDTSGYYQRMLVVLLQANRDPDTAIDDAQVELDAQALFQAGELKWGTDEEEFITILGTRSVSHLRRVFDKYMTISGFQIEETIDRETSGNLENLLLAVVKSIRSIPAYLAETLYYAMKGAGTDDHTLIRVIVSRSEIDLFNIRKEFRKNFATSLYSMIKGDTSGDYKKALLLLSGGEDD

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
宿主生物 host_organism	Escherichia coli

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	22

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	147

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7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d2h0ka_
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

Domain ID domain_id	d2h0kb_
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 (8 domains)

Domain ID domain_id	2h0kA01
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	2h0kA02
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	2h0kA03
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	2h0kA04
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	2h0kB01
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	2h0kB02
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	2h0kB03
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	2h0kB04
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	51.108 Å
Unit-cell length b length_b	67.184 Å
Unit-cell length c length_c	112.313 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.79 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.760 Å
Low-resolution limit resolution_low	33.590 Å
R factor r_factor	0.2010
R_work r_work	0.1970
R_free r_free	0.2610

fit	/app/data/saxs_computation/h0/2h0k/2h0k.fit
pddf	/app/data/pr_computation/h0/2h0k/2h0k.pr.out
profile	/app/data/saxs_computation/h0/2h0k/2h0k.dat

Crystal Structure of a Mutant of Rat Annexin A5

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