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Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF METHYLATED PVS25, AN OOKINETE PROTEIN FROM PLASMODIUM VIVAX

Authors :   A. K. Saxena, K. Singh, H. P. Su, M. M. Klein, A. W. Stowers, A. J. Saul, C. A. Long, D. N. Garboczi

Date :   07 Mar 05 (Deposition) - 06 Dec 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A,B

Keywords :   Four Egf-Like Domains, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. K. Saxena, K. Singh, H. P. Su, M. M. Klein, A. W. Stowers, A. J. Saul, C. A. Long, D. N. Garboczi
The Essential Mosquito-Stage P25 And P28 Proteins From Plasmodium Form Tile-Like Triangular Prisms
Nat. Struct. Mol. Biol. V. 13 90 2006
PubMed-ID: 16327807 | Reference-DOI: 10.1038/NSMB1024
(for further references see the PDB file header)

Molecule 1 - OOKINETE SURFACE PROTEIN PVS25
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	SACCHAROMYCES CEREVISIAE
	Expression System Common	:	BAKER'S YEAST
	Expression System Plasmid	:	YEPRPEU-3
	Expression System Strain	:	S. CEREVISIAE VK1
	Expression System Taxid	:	4932
	Expression System Vector Type	:	PLASMID
	Organism Common	:	MALARIA PARASITE P. VIVAX
	Organism Scientific	:	PLASMODIUM VIVAX
	Organism Taxid	:	5855

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 45)

No.	Name	Count	Type	Full Name
1	MLY	36	Mod. Amino Acid	N-DIMETHYL-LYSINE
2	YB	9	Ligand/Ion	YTTERBIUM (III) ION

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:168	BINDING SITE FOR RESIDUE YB A 182
2	AC2	SOFTWARE	GLU A:38 , ASP A:125 , GLU A:126 , HOH A:199	BINDING SITE FOR RESIDUE YB A 183
3	AC3	SOFTWARE	ASP B:82 , HOH B:208	BINDING SITE FOR RESIDUE YB B 182
4	AC4	SOFTWARE	YB A:185 , YB A:186 , YB A:187 , GLU B:161	BINDING SITE FOR RESIDUE YB A 184
5	AC5	SOFTWARE	YB A:184 , YB A:186 , YB A:187	BINDING SITE FOR RESIDUE YB A 185
6	AC6	SOFTWARE	YB A:184 , YB A:185 , YB A:187 , GLU B:161	BINDING SITE FOR RESIDUE YB A 186
7	AC7	SOFTWARE	GLU A:107 , YB A:184 , YB A:185 , YB A:186 , GLU B:161	BINDING SITE FOR RESIDUE YB A 187
8	AC8	SOFTWARE	ASP A:62	BINDING SITE FOR RESIDUE YB A 188
9	AC9	SOFTWARE	ASP B:87	BINDING SITE FOR RESIDUE YB B 183

Asymmetric/Biological Unit

No.	Residues
1	A:8	-	A:22
2	A:24	-	A:36
3	A:42	-	A:57
4	A:51	-	A:71
5	A:73	-	A:84
6	A:89	-	A:100
7	A:94	-	A:113
8	A:115	-	A:129
9	A:137	-	A:148
10	A:141	-	A:157
11	A:159	-	A:172
12	B:8	-	B:22
13	B:24	-	B:36
14	B:42	-	B:57
15	B:51	-	B:71
16	B:73	-	B:84
17	B:89	-	B:100
18	B:94	-	B:113
19	B:115	-	B:129
20	B:137	-	B:148
21	B:141	-	B:157
22	B:159	-	B:172

(no "Cis Peptide Bond" information available for 1Z1Y)

(no "SAP(SNP)/Variant" information available for 1Z1Y)

(no "PROSITE Motif" information available for 1Z1Y)

(no "Exon" information available for 1Z1Y)

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
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Chain A from PDB  Type:PROTEIN  Length:177
 aligned with O96555_PLAVI | O96555 from UniProtKB/TrEMBL  Length:219

    Alignment length:177
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       
         O96555_PLAVI    23 AVTVDTICKNGQLVQMSNHFKCMCNEGLVHLSENTCEEKNECKKETLGKACGEFGQCIENPDPAQVNMYKCGCIEGYTLKEDTCVLDVCQYKNCGESGECIVEYLSEIQSAGCSCAIGKVPNPEDEKKCTKTGETACQLKCNTDNEVCKNVEGVYKCQCMEGFTFDKEKNVCLSYSV 199
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeee....eeeee...eeeee..eeee....hhhhh..eee..eeeee.........eeeee...eeee..eeee.hhh.......eeeeeeee..eeeeeeee..eee..........eee............eeeeee..eeeeee....eee....eee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z1y A   1 AVTVDTICkNGQLVQMSNHFkCMCNEGLVHLSENTCEEkNECkkETLGkACGEFGQCIENPDPAQVNMYkCGCIEGYTLkEDTCVLDVCQYkNCGESGECIVEYLSEIQSAGCSCAIGkVPNPEDEkkCTkTGETACQLkCNTDNEVCkNVEGVYkCQCMEGFTFDkEkNVCLGPHH 177
                                    10        20|       30        40  ||    50        60        70        80        90 |     100       110       120      |130|      140       150     | 160      |170       
                                    9-MLY      21-MLY            39-MLY|    |                   70-MLY    80-MLY      92-MLY                    119-MLY 127-MLY      140-MLY  149-MLY  |        167-MLY      
                                                                     43-MLY |                                                                            128-MLY                     156-MLY      169-MLY    
                                                                      44-MLY|                                                                               131-MLY                                          
                                                                           49-MLY

Chain B from PDB  Type:PROTEIN  Length:175
 aligned with O96555_PLAVI | O96555 from UniProtKB/TrEMBL  Length:219

    Alignment length:175
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192     
         O96555_PLAVI    23 AVTVDTICKNGQLVQMSNHFKCMCNEGLVHLSENTCEEKNECKKETLGKACGEFGQCIENPDPAQVNMYKCGCIEGYTLKEDTCVLDVCQYKNCGESGECIVEYLSEIQSAGCSCAIGKVPNPEDEKKCTKTGETACQLKCNTDNEVCKNVEGVYKCQCMEGFTFDKEKNVCLSY 197
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Plasmod_Pvs28-1z1yB01 B:1-173                                                                                                                                                -- Pfam domains (1)
           Pfam domains (2) Plasmod_Pvs28-1z1yB02 B:1-173                                                                                                                                                -- Pfam domains (2)
         Sec.struct. author ..........eeeee....eeeee....eeee..eee.....hhhhh..eee..eeeee.........eeeee...eeee..eeee.hhh.......eeeeeee....eeeeeee..eee..........eee............eeeeee..eeeeee....eee....eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z1y B   1 AVTVDTICkNGQLVQMSNHFkCMCNEGLVHLSENTCEEkNECkkETLGkACGEFGQCIENPDPAQVNMYkCGCIEGYTLkEDTCVLDVCQYkNCGESGECIVEYLSEIQSAGCSCAIGkVPNPEDEkkCTkTGETACQLkCNTDNEVCkNVEGVYkCQCMEGFTFDkEkNVCLGP 175
                                    10        20|       30        40  ||    50        60        70        80        90 |     100       110       120      |130|      140       150     | 160      |170     
                                    9-MLY      21-MLY            39-MLY|    |                   70-MLY    80-MLY      92-MLY                    119-MLY 127-MLY      140-MLY  149-MLY  |        167-MLY    
                                                                     43-MLY |                                                                            128-MLY                     156-MLY      169-MLY  
                                                                      44-MLY|                                                                               131-MLY                                        
                                                                           49-MLY

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 '\|'

(no "SCOP Domain" information available for 1Z1Y)

(no "CATH Domain" information available for 1Z1Y)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Plasmod_Pvs28] (3)

Family: Plasmod_Pvs28 (3)

Plasmodium vivax (3)

1a	Plasmod_Pvs28-1z1yB01	B:1-173
1b	Plasmod_Pvs28-1z1yB02	B:1-173

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (O96555_PLAVI | O96555)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
cellular component
	GO:0009986	cell surface	The external part of the cell wall and/or plasma membrane.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Asymmetric/Biological Unit
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 45)

Sites (9, 9)

SS Bonds (22, 22)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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