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

Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF ADENOSINE DEAMINASE FROM PLASMODIUM VIVAX IN COMPLEX WITH ADENOSINE

Authors :   E. T. Larson, E. A. Merritt, Structural Genomics Of Pathogenic Pro Consortium (Sgpp)

Date :   09 Apr 07 (Deposition) - 24 Apr 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.89

Chains :   Asym./Biol. Unit : A

Keywords :   Metallo-Dependent Hydrolase, Structural Genomics, Medical Structural Genomics Of Pathogenic Protozoa Consortium, Msgpp, Structural Genomics Of Pathogenic Protozoa Consortium, Sgpp, Psi, Protein Structure Initiative, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. T. Larson, W. Deng, B. E. Krumm, A. Napuli, N. Mueller, W. C. Van Voorhis, F. S. Buckner, E. Fan, A. Lauricella, G. Detitta, J. Luft, F. Zucker, W. G. Hol, C. L. Verlinde, E. A. Merritt
Structures Of Substrate- And Inhibitor-Bound Adenosine Deaminase From A Human Malaria Parasite Show A Dramatic Conformational Change And Shed Light On Drug Selectivity.
J. Mol. Biol. V. 381 975 2008
PubMed-ID: 18602399 | Reference-DOI: 10.1016/J.JMB.2008.06.048

Molecule 1 - ADENOSINE DEAMINASE
	Chains	:	A
	EC Number	:	3.5.4.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	BG1861
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	PV111245
	Organism Common	:	MALARIA PARASITE P. VIVAX
	Organism Scientific	:	PLASMODIUM VIVAX
	Organism Taxid	:	5855

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 13)

No.	Name	Count	Type	Full Name
1	ADN	1	Ligand/Ion	ADENOSINE
2	CCN	2	Ligand/Ion	ACETONITRILE
3	MSE	9	Mod. Amino Acid	SELENOMETHIONINE
4	ZN	1	Ligand/Ion	ZINC ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:42 , HIS A:44 , HIS A:226 , HIS A:253 , ASP A:310 , ADN A:501	BINDING SITE FOR RESIDUE ZN A 401
2	AC2	SOFTWARE	HIS A:44 , ASP A:46 , LEU A:85 , PHE A:88 , ILE A:170 , ASP A:172 , GLY A:201 , HIS A:226 , GLU A:229 , HIS A:253 , ASP A:310 , ASP A:311 , ZN A:401 , HOH A:642 , HOH A:649	BINDING SITE FOR RESIDUE ADN A 501
3	AC3	SOFTWARE	VAL A:149 , LYS A:153 , HOH A:666 , HOH A:805	BINDING SITE FOR RESIDUE CCN A 601
4	AC4	SOFTWARE	GLN A:261 , LYS A:268 , ALA A:301 , HOH A:658	BINDING SITE FOR RESIDUE CCN A 602

(no "SS Bond" information available for 2PGF)

(no "Cis Peptide Bond" information available for 2PGF)

(no "SAP(SNP)/Variant" information available for 2PGF)

(no "PROSITE Motif" information available for 2PGF)

(no "Exon" information available for 2PGF)

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:359
 aligned with A5KE01_PLAVS | A5KE01 from UniProtKB/TrEMBL  Length:363

    Alignment length:359
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354         
         A5KE01_PLAVS     5 QEPIDFLKKEELKNIDLSQMSKKERYKIWKRIPKCELHCHLDLCFSADFFVSCIRKYNLQPNLSDEEVLDYYLFAKGGKSLGEFVEKAIKVADIFHDYEVIEDLAKHAVFNKYKEGVVLMEFRYSPTFVAFKYNLDIELIHQAIVKGIKEVVELLDHKIHVALMCIGDTGHEAANIKASADFCLKHKADFVGFDHGGHEVDLKEYKEIFDYVRESGVPLSVHAGEDVTLPNLNTLYSAIQVLKVERIGHGIRVAESQELIDMVKEKNILLEVCPISNVLLKNAKSMDTHPIRQLYDAGVKVSVNSDDPGMFLTNINDDYEELYTHLNFTLEDFMKMNEWALEKSFMDSNIKDKIKNLYF 363
               SCOP domains d2pgfa_ A: automated matches                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------A_deaminase-2pgfA01 A:35-361                                                                                                                                                                                                                                                                                                           -- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.hhh.hhhhhhhhhhhh......hhhhhhhhhh......hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhheeeeeeeehhhhhhh....hhhhhhhhhhhhhhhhhhhh....eeeeeeeeee.....hhhhhhhhhhhh...eeeeeeee...hhhhhhhhhhhhhhh....eeee........hhhhhhhhhh....eeee.hhhhhhhhhhhhhhhh..eeeehhhhhhhh....hhhhhhhhhhhhh..eeee...hhhhhh.hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pgf A   5 QEPIDFLKKEELKNIDLSQmSKKERYKIWKRIPKCELHCHLDLCFSADFFVSCIRKYNLQPNLSDEEVLDYYLFAKGGKSLGEFVEKAIKVADIFHDYEVIEDLAKHAVFNKYKEGVVLmEFRYSPTFVAFKYNLDIELIHQAIVKGIKEVVELLDHKIHVALmCIGDTGHEAANIKASADFCLKHKADFVGFDHGGHEVDLKEYKEIFDYVRESGVPLSVHAGEDVTLPNLNTLYSAIQVLKVERIGHGIRVAESQELIDmVKEKNILLEVCPISNVLLKNAKSmDTHPIRQLYDAGVKVSVNSDDPGmFLTNINDDYEELYTHLNFTLEDFmKmNEWALEKSFmDSNIKDKIKNLYF 363
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164   |   174       184       194       204       214       224       234       244       254       264 |     274       284     | 294       304       314       324       334   | | 344     | 354         
                                              24-MSE                                                                                             124-MSE                                     168-MSE                                                                                           266-MSE                 290-MSE                 314-MSE                 338-MSE     350-MSE         
                                                                                                                                                                                                                                                                                                                                                                         340-MSE

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: Alpha and beta proteins (a/b) (23833)

Fold: TIM beta/alpha-barrel (3956)

Superfamily: Metallo-dependent hydrolases (273)

Family: Adenosine/AMP deaminase (36)

Protein domain: automated matches (11)

Plasmodium vivax [TaxId: 5855] (4)

d2pgfa_

(no "CATH Domain" information available for 2PGF)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Amidohydrolase (126)

Family: A_deaminase (23)

Plasmodium vivax (strain Salvador I) (3)

A_deaminase-2pgfA01

A:35-361

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (A5KE01_PLAVS | A5KE01)

molecular function
	GO:0019239	deaminase activity	Catalysis of the removal of an amino group from a substrate, producing ammonia (NH3).
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0009168	purine ribonucleoside monophosphate biosynthetic process	The chemical reactions and pathways resulting in the formation of purine ribonucleoside monophosphate, a compound consisting of a purine base linked to a ribose sugar esterified with phosphate on the sugar.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2pgf)

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	3.5.4.4
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	A5KE01_PLAVS \| A5KE01	:	2pgr 2qvn 3ewc 3ewd

2pgr	CRYSTAL STRUCTURE OF ADENOSINE DEAMINASE FROM PLASMODIUM VIVAX IN COMPLEX WITH INHIBITOR, PENTOSTATIN
2qvn	CRYSTAL STRUCTURE OF ADENOSINE DEAMINASE FROM PLASMODIUM VIVAX IN COMPLEX WITH GUANOSINE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 13)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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SCOP Domains (1, 1)

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Related Entries

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