1YII - JenaLib

Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURES OF CHICKEN ANNEXIN V IN COMPLEX WITH CA2+

Authors :   E. A. Ortlund, G. Chai, B. Genge, L. N. Y. Wu, R. E. Wuthier, L. Lebioda

Date :   11 Jan 05 (Deposition) - 08 Mar 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.42

Chains :   Asym./Biol. Unit : A

Keywords :   Annexin; Membrane Binding; Matrix Vessicle, Protein And Metal Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. A. Ortlund, G. Chai, B. Genge, L. N. Y. Wu, R. E. Wuthier, L. Lebioda
Crystal Structures Of Chicken Annexin A5 In Complex With Functional Modifiers Ca2+ And Zn2+ Reveal Zn2+ Induced Formation Of Non-Planar Assemblies
Annexins V. 1 183 2005
PubMed: search
(for further references see the PDB file header)

Molecule 1 - ANNEXIN A5
	Chains	:	A
	Organism Common	:	CHICKEN
	Organism Scientific	:	GALLUS GALLUS
	Organism Taxid	:	9031
	Other Details	:	GENE ANXA5, ANX5
	Synonym	:	ANNEXIN V; LIPOCORTIN V; ENDONEXIN II

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 6)

No.	Name	Count	Type	Full Name
1	CA	3	Ligand/Ion	CALCIUM ION
2	SO4	3	Ligand/Ion	SULFATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:25 , GLY A:30 , HOH A:584	BINDING SITE FOR RESIDUE SO4 A 501
2	AC2	SOFTWARE	LYS A:70 , ARG A:86 , HIS A:94 , HOH A:508 , HOH A:578 , HOH A:696 , HOH A:730 , HOH A:816	BINDING SITE FOR RESIDUE SO4 A 502
3	AC3	SOFTWARE	SER A:13 , PRO A:14 , PHE A:15 , SER A:146 , GLY A:147 , ARG A:151 , HOH A:637	BINDING SITE FOR RESIDUE SO4 A 503
4	AC4	SOFTWARE	MET A:28 , GLY A:30 , GLY A:32 , GLU A:72 , HOH A:744	BINDING SITE FOR RESIDUE CA A 401
5	AC5	SOFTWARE	ILE A:100 , GLY A:102 , GLY A:104 , GLU A:144 , HOH A:787	BINDING SITE FOR RESIDUE CA A 402
6	AC6	SOFTWARE	MET A:259 , GLY A:261 , GLY A:263 , ASP A:303 , HOH A:779 , HOH A:780	BINDING SITE FOR RESIDUE CA A 403

(no "SS Bond" information available for 1YII)

Asymmetric/Biological Unit

No.	Residues
1	Ser A:13	-	Pro A:14

(no "SAP(SNP)/Variant" information available for 1YII)

Asymmetric/Biological Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ANNEXIN	PS00223	Annexins repeated domain signature.	ANXA5_CHICK	32-84 104-156 188-240 263-315	4	A:32-84 A:104-156 A:188-240 A:263-315

(no "Exon" information available for 1YII)

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:316
 aligned with ANXA5_CHICK | P17153 from UniProtKB/Swiss-Prot  Length:321

    Alignment length:316
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311      
          ANXA5_CHICK     2 AKYTRGTVTAFSPFDARADAEALRKAMKGMGTDEETILKILTSRNNAQRQEIASAFKTLFGRDLVDDLKSELTGKFETLMVSLMRPARIFDAHALKHAIKGAGTNEKVLTEILASRTPAEVQNIKQVYMQEYEANLEDKITGETSGHFQRLLVVLLQANRDPDGRVDEALVEKDAQVLFRAGELKWGTDEETFITILGTRSVSHLRRVFDKYMTISGFQIEETIDRETSGDLEKLLLAVVKCIRSVPAYFAETLYYSMKGAGTDDDTLIRVMVSRSEIDLLDIRHEFRKNFAKSLYQMIQKDTSGDYRKALLLLCG 317
               SCOP domains d1yiia_ A: Annexin V                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ------------1yiiA01 A:14-86  [code=1.10.220.10, no name defined]                     1yiiA02 A:87-160  [code=1.10.220.10, no name defined]                     1yiiA03 A:161-246  [code=1.10.220.10, no name defined]                                1yiiA04 A:247-317  [code=1.10.220.10, no name defined]                  CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Annexin-1yiiA01 A:250-315                                         -- Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Annexin-1yiiA02 A:250-315                                         -- Pfam domains (2)
           Pfam domains (3) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Annexin-1yiiA03 A:250-315                                         -- Pfam domains (3)
           Pfam domains (4) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Annexin-1yiiA04 A:250-315                                         -- Pfam domains (4)
         Sec.struct. author ..............hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------ANNEXIN  PDB: A:32-84 UniProt: 32-84                 -------------------ANNEXIN  PDB: A:104-156 UniProt: 104-156             -------------------------------ANNEXIN  PDB: A:188-240 UniProt: 188-240             ----------------------ANNEXIN  PDB: A:263-315 UniProt: 263-315             -- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yii A   2 AKYTRGTVTAFSPFDARADAEALRKAMKGMGTDEETILKILTSRNNAQRQEIASAFKTLFGRDLVDDLKSELTGKFETLMVSLMRPARIFDAHALKHAIKGAGTNEKVLTEILASRTPAEVQNIKQVYMQEYEANLEDKITGETSGHFQRLLVVLLQANRDPDGRVDEALVEKDAQVLFRAGELKWGTDEETFITILGTRSVSHLRRVFDKYMTISGFQIEETIDRETSGDLEKLLLAVVKCIRSVPAYFAETLYYSMKGAGTDDDTLIRVMVSRSEIDLLDIRHEFRKNFAKSLYQMIQKDTSGDYRKALLLLCG 317
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Annexin (61)

Superfamily: Annexin (61)

Family: Annexin (56)

Protein domain: Annexin V (31)

Chicken (Gallus gallus) [TaxId: 9031] (3)

d1yiia_

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Annexin V; domain 1 (80)

Homologous Superfamily: [code=1.10.220.10, no name defined] (58)

Chicken (Gallus gallus) (3)

1a	1yiiA02	A:87-160
1b	1yiiA01	A:14-86
1c	1yiiA04	A:247-317
1d	1yiiA03	A:161-246

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Annexin] (14)

Family: Annexin (14)

Gallus gallus (Chicken) (2)

1a	Annexin-1yiiA01	A:250-315
1b	Annexin-1yiiA02	A:250-315
1c	Annexin-1yiiA03	A:250-315
1d	Annexin-1yiiA04	A:250-315

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (ANXA5_CHICK | P17153)

molecular function
	GO:0005262	calcium channel activity	Enables the facilitated diffusion of a calcium ion (by an energy-independent process) involving passage through a transmembrane aqueous pore or channel without evidence for a carrier-mediated mechanism.
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0005544	calcium-dependent phospholipid binding	Interacting selectively and non-covalently with phospholipids, a class of lipids containing phosphoric acid as a mono- or diester, in the presence of calcium.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0055074	calcium ion homeostasis	Any process involved in the maintenance of an internal steady state of calcium ions within an organism or cell.
	GO:0070588	calcium ion transmembrane transport	A process in which a calcium ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
	GO:0050819	negative regulation of coagulation	Any process that stops, prevents, or reduces the frequency, rate or extent of coagulation.
cellular component
	GO:0034704	calcium channel complex	An ion channel complex through which calcium ions pass.
	GO:0031982	vesicle	Any small, fluid-filled, spherical organelle enclosed by membrane.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ser A:13 - Pro A:14	[ RasMol ]

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	1yii
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	ANXA5_CHICK \| P17153	:	1ala 1yj0

1yj0	ANNEXIN A5 IN COMPLEX WITH ZINC

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 4)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 1)

CATH Domains (1, 4)

Pfam Domains (1, 4)

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