SAXSdb — 1avr

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

ANNEXIN V

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 1–319	Not recorded	CA CALCIUM ION × 5 SO4 SULFATE ION × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.30 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 1AVR	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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion	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 ligand/ion	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	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	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
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 ligand/ion 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 ligand/ion	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 ligand/ion 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 ligand/ion 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 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 construct 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
6K25 Crystal structure of Ca-unbound human Annexin A5 in low salt condition Deposited 2019-05-13	Different construct 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	No recorded non-water small molecule	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
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 construct 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 construct 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 2–320； UniProt 1–319

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	1avr
Deposition date deposition_date	1991-10-17
Structure title title	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
Keywords keywords	CALCIUM/PHOSPHOLIPID BINDING, CALCIUM-PHOSPHOLIPID BINDING complex; CALCIUM/PHOSPHOLIPID BINDING
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	22.48 Å
Radius of gyration Rg (electron density) rg_electron	21.51 Å
Forward intensity I(0) i0	22266900.00
Molecular weight molecular_weight	35884.0 kDa
Excluded volume excluded_volume	44919 Å³
Envelope volume envelope_volume	52965 Å³
Hydration-shell volume shell_volume	21336 Å³
Envelope diameter envelope_diameter	77.8 Å
Shell Rg shell_rg	27.69 Å
Envelope Rg envelope_rg	21.66 Å
Shape Rg shape_rg	21.49 Å
Total Rg total_rg	22.38 Å
Total atoms total_atoms	2512
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	78.5 Å
Rg (real space) rg_real	22.52 Å
Rg uncertainty (real space) rg_real_error	0.47 Å
I(0) (real space) i0_real	2.2270e+07
I(0) uncertainty (real space) i0_real_error	2.9460e+05
Rg (reciprocal space) rg_reciprocal	22.51 Å
I(0) (reciprocal space) i0_reciprocal	22270000.0000
Solution quality estimate total_estimate	0.8569
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	25.0 Å
Skewness Skewness skewness	0.455
Kurtosis Kurtosis kurtosis	-0.068
Angular range angular_range	— – 0.3550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	6243000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.728; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.966; Smooth: 0.987

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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	35980.7 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	2714

MAQVLRGTVTDFPGFDERADAETLRKAMKGLGTDEESILTLLTSRSNAQRQEISAAFKTLFGRDLLDDLKSELTGKFEKLIVALMKPSRLYDAYELKHALKGAGTNEKVLTEIIASRTPEELRAIKQVYEEEYGSSLEDDVVGDTSGYYQRMLVVLLQANRDPDAGIDEAQVEQDAQALFQAGELKWGTDEEKFITIFGTRSVSHLRKVFDKYMTISGFQIEETIDRETSGNLEQLLLAVVKSIRSIPAYLAETLYYAMKGAGTDDHTLIRVMVSRSEIDLFNIRKEFRKNFATSLYSMIKGDTSGDYKKALLLLCGEDD

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606

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	5

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	202

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7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1avra_
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	1avrA01
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	1avrA02
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	1avrA03
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	1avrA04
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 (3)

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Unit-cell length a length_a	99.700 Å
Unit-cell length b length_b	99.700 Å
Unit-cell length c length_c	96.350 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	2.300 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	0.1840
R_free r_free	—

fit	/app/data/saxs_computation/av/1avr/1avr.fit
pddf	/app/data/pr_computation/av/1avr/1avr.pr.out
profile	/app/data/saxs_computation/av/1avr/1avr.dat

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