SAXSdb — 6k25

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

Annexin A5

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 2–320	Not recorded	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；288 K；0.2 M Sodium phosphate dibasic dehydrate 20% w/v Polyethylene glycol 3,350 2 mM TCEP	Resolution 2.40 Å R-free 0.292

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 6K25	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1ANW THE EFFECT OF METAL BINDING ON THE STRUCTURE OF ANNEXIN V AND IMPLICATIONS FOR MEMBRANE BINDING Deposited 1993-10-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–319（319 aa）	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å
1ANW THE EFFECT OF METAL BINDING ON THE STRUCTURE OF ANNEXIN V AND IMPLICATIONS FOR MEMBRANE BINDING Deposited 1993-10-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–319（319 aa）	Not recorded	CA CALCIUM ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.40 Å
1ANX THE CRYSTAL STRUCTURE OF A NEW HIGH-CALCIUM FORM OF ANNEXIN V Deposited 1993-10-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–319（319 aa）	Not recorded	CA CALCIUM ION × 4 SO4 SULFATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å
1ANX THE CRYSTAL STRUCTURE OF A NEW HIGH-CALCIUM FORM OF ANNEXIN V Deposited 1993-10-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–319（319 aa）	Not recorded	CA CALCIUM ION × 4 SO4 SULFATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å
1ANX THE CRYSTAL STRUCTURE OF A NEW HIGH-CALCIUM FORM OF ANNEXIN V Deposited 1993-10-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–319（319 aa）	Not recorded	CA CALCIUM ION × 4 SO4 SULFATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 1.90 Å
1AVH CRYSTAL AND MOLECULAR STRUCTURE OF HUMAN ANNEXIN V AFTER REFINEMENT. IMPLICATIONS FOR STRUCTURE, MEMBRANE BINDING AND ION CHANNEL FORMATION OF THE ANNEXIN FAMILY OF PROTEINS Deposited 1991-10-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–319（319 aa）	Not recorded	CA CALCIUM ION × 3 SO4 SULFATE ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
1AVH CRYSTAL AND MOLECULAR STRUCTURE OF HUMAN ANNEXIN V AFTER REFINEMENT. IMPLICATIONS FOR STRUCTURE, MEMBRANE BINDING AND ION CHANNEL FORMATION OF THE ANNEXIN FAMILY OF PROTEINS Deposited 1991-10-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–319（319 aa）	Not recorded	CA CALCIUM ION × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
1AVH CRYSTAL AND MOLECULAR STRUCTURE OF HUMAN ANNEXIN V AFTER REFINEMENT. IMPLICATIONS FOR STRUCTURE, MEMBRANE BINDING AND ION CHANNEL FORMATION OF THE ANNEXIN FAMILY OF PROTEINS Deposited 1991-10-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–319（319 aa） Chain B 1–319（319 aa）	Not recorded	CA CALCIUM ION × 5 SO4 SULFATE ION × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
1AVH CRYSTAL AND MOLECULAR STRUCTURE OF HUMAN ANNEXIN V AFTER REFINEMENT. IMPLICATIONS FOR STRUCTURE, MEMBRANE BINDING AND ION CHANNEL FORMATION OF THE ANNEXIN FAMILY OF PROTEINS Deposited 1991-10-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–319（319 aa） Chain B 1–319（319 aa）	Not recorded	CA CALCIUM ION × 5 SO4 SULFATE ION × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
1AVR CRYSTAL AND MOLECULAR STRUCTURE OF HUMAN ANNEXIN V AFTER REFINEMENT. IMPLICATIONS FOR STRUCTURE, MEMBRANE BINDING AND ION CHANNEL FORMATION OF THE ANNEXIN FAMILY OF PROTEINS Deposited 1991-10-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–319（319 aa）	Not recorded	CA CALCIUM ION × 5 SO4 SULFATE ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
1HAK CRYSTAL STRUCTURE OF RECOMBINANT HUMAN PLACENTAL ANNEXIN V COMPLEXED WITH K-201 AS A CALCIUM CHANNEL ACTIVITY INHIBITOR Deposited 1997-12-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–319（319 aa） Fragment：ANNEXIN FOLD Chain B 1–319（319 aa） Fragment：ANNEXIN FOLD	Not recorded	K21 4-[3-{1-(4-BENZYL)PIPERODINYL}PROPIONYL]-7-METHOXY-2,3,4,5-TERTRAHYDRO-1,4-BENZOTHIAZEPINE × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；pH 7.5	Resolution 3.00 Å R-free 0.331
1HVD STRUCTURAL AND ELECTROPHYSIOLOGICAL ANALYSIS OF ANNEXIN V MUTANTS. MUTAGENESIS OF HUMAN ANNEXIN V, AN IN VITRO VOLTAGE-GATED CALCIUM CHANNEL, PROVIDES INFORMATION ABOUT THE STRUCTURAL FEATURES OF THE ION PATHWAY, THE VOLTAGE SENSOR AND THE ION SELECTIVITY FILTER Deposited 1994-06-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–319（319 aa）	Not recorded	CA CALCIUM ION × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å
1HVE STRUCTURAL AND ELECTROPHYSIOLOGICAL ANALYSIS OF ANNEXIN V MUTANTS. MUTAGENESIS OF HUMAN ANNEXIN V, AN IN VITRO VOLTAGE-GATED CALCIUM CHANNEL, PROVIDES INFORMATION ABOUT THE STRUCTURAL FEATURES OF THE ION PATHWAY, THE VOLTAGE SENSOR AND THE ION SELECTIVITY FILTER Deposited 1994-06-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–319（319 aa）	Not recorded	CA CALCIUM ION × 5 SO4 SULFATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.30 Å
1HVF STRUCTURAL AND ELECTROPHYSIOLOGICAL ANALYSIS OF ANNEXIN V MUTANTS. MUTAGENESIS OF HUMAN ANNEXIN V, AN IN VITRO VOLTAGE-GATED CALCIUM CHANNEL, PROVIDES INFORMATION ABOUT THE STRUCTURAL FEATURES OF THE ION PATHWAY, THE VOLTAGE SENSOR AND THE ION SELECTIVITY FILTER Deposited 1994-06-29	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–319（319 aa）	Not recorded	CA CALCIUM ION × 5 SO4 SULFATE ION × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.00 Å
1HVG STRUCTURAL AND ELECTROPHYSIOLOGICAL ANALYSIS OF ANNEXIN V MUTANTS. MUTAGENESIS OF HUMAN ANNEXIN V, AN IN VITRO VOLTAGE-GATED CALCIUM CHANNEL, PROVIDES INFORMATION ABOUT THE STRUCTURAL FEATURES OF THE ION PATHWAY, THE VOLTAGE SENSOR AND THE ION SELECTIVITY FILTER Deposited 1994-06-29	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–319（319 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 3.00 Å
1SAV HUMAN ANNEXIN V WITH PROLINE SUBSTITUTION BY THIOPROLINE Deposited 1997-11-24	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：P13, P87, P119, P163, AND P248 SUBSTITUTED WITH THIOPROLINE (PRS) Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；PROTEIN WAS CRYSTALLIZED FROM 2.1 M AMMONIUM SULFATE, 0.1 M TRIS-HCL, PH 8.5	Resolution 2.50 Å R-free 0.259
2XO2 Human Annexin V with incorporated Methionine analogue Azidohomoalanine Deposited 2010-08-09	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 1–320（320 aa）	Mutation：YES Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 2 NA SODIUM ION × 1 SO4 SULFATE ION × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；2.0 M AMMONIUM SULFATE, 20 MM CALCIUM CHLORIDE, 0.1 M TRIS/HCL, PH 8.5	Resolution 2.80 Å R-free 0.296
2XO3 Human Annexin V with incorporated Methionine analogue Homopropargylglycine Deposited 2010-08-09	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 1–320（320 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	CA CALCIUM ION × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；2.0 M AMMONIUM SULFATE, 20 MM CALCIUM CHLORIDE, 0.1 M TRIS/HCL, PH 8.5	Resolution 2.30 Å R-free 0.291
6K22 Crystal structure of Ca-bound human Annexin A5 in low salt condition Deposited 2019-05-13	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–320（319 aa）	Not recorded	CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；287 K；0.2 M Potassium Citrate Tribasic pH 8.3 0.1 M HEPES pH 7.5 17% PEG3350 50uM CaCl2 2mM TCEP	Resolution 2.75 Å R-free 0.306
8GYC Annexin A5 protein dimer mutant Deposited 2022-09-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–320（319 aa） Chain B 2–320（319 aa）	Not recorded	CA CALCIUM ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289.15 K；PEG 3350, sodium chloride, 2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid	Resolution 1.80 Å R-free 0.288
8H0J Annexin A5 mutant Deposited 2022-09-29	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–320（319 aa）	Not recorded	CA CALCIUM ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289.15 K；PEG 3350, sodium chloride, 2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid	Resolution 2.23 Å R-free 0.246
8H9Z Annexin A5 protein mutant Deposited 2022-10-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–320（319 aa）	Not recorded	CA CALCIUM ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289.15 K；PEG 3350, sodium chloride, 2-[4-(2-hydroxyethyl)piperazin-1-yl]ethanesulfonic acid	Resolution 1.42 Å R-free 0.265

16 other PDB entries and 22 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ANXA5_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–321； UniProt 2–320

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	6k25
Deposition date deposition_date	2019-05-13
Structure title title	Crystal structure of Ca-unbound human Annexin A5 in low salt condition
Keywords keywords	Annexin A5, phospholipid binding, membrane repair, AnxA5, LIPID BINDING PROTEIN; LIPID 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	22.41 Å
Radius of gyration Rg (electron density) rg_electron	21.43 Å
Forward intensity I(0) i0	21465400.00
Molecular weight molecular_weight	35348.0 kDa
Excluded volume excluded_volume	44397 Å³
Envelope volume envelope_volume	52948 Å³
Hydration-shell volume shell_volume	21351 Å³
Envelope diameter envelope_diameter	76.0 Å
Shell Rg shell_rg	27.64 Å
Envelope Rg envelope_rg	21.59 Å
Shape Rg shape_rg	21.43 Å
Total Rg total_rg	22.25 Å
Total atoms total_atoms	2487
Residues n_residues	315
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	76.0 Å
Rg (real space) rg_real	22.44 Å
Rg uncertainty (real space) rg_real_error	0.62 Å
I(0) (real space) i0_real	2.1470e+07
I(0) uncertainty (real space) i0_real_error	3.0410e+05
Rg (reciprocal space) rg_reciprocal	22.43 Å
I(0) (reciprocal space) i0_reciprocal	21470000.0000
Solution quality estimate total_estimate	0.8721
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.3 Å
Skewness Skewness skewness	0.451
Kurtosis Kurtosis kurtosis	-0.091
Angular range angular_range	— – 0.3550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6053000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.784; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.997

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d6k25a_
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	6k25A01
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	6k25A02
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	6k25A03
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	6k25A04
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	94.512 Å
Unit-cell length b length_b	94.512 Å
Unit-cell length c length_c	136.701 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	12

Space group space_group	P 63 2 2
Space-group number int_tables_number	182
Crystal system crystal_system	—

Resolution resolution	2.401 Å
Low-resolution limit resolution_low	38.870 Å
R factor r_factor	0.2302
R_work r_work	0.2270
R_free r_free	0.2919

Description description	Annexin A5
Molecular weight formula_weight	37419.2 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	2525

Crystal structure of Ca-unbound human Annexin A5 in low salt condition

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (1 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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 BL21

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	38

fit	/app/data/saxs_computation/k2/6k25/6k25.fit
pddf	/app/data/pr_computation/k2/6k25/6k25.pr.out
profile	/app/data/saxs_computation/k2/6k25/6k25.dat