2QVN - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

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

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

Date :   08 Aug 07 (Deposition) - 04 Sep 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.19

Chains :   Asym./Biol. Unit : A

Keywords :   Metallo-Dependent Hydrolase, Tim Barrel, Structural Genomics, Medical Structural Genomics Of Pathogenic Protozoa Consortium, Msgpp, Plasmodium, Malaria, 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, PVX_111245
	Organism Scientific	:	PLASMODIUM VIVAX SAI-1
	Organism Taxid	:	126793
	Strain	:	SALVADOR I

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 11)

No.	Name	Count	Type	Full Name
1	GMP	1	Ligand/Ion	GUANOSINE
2	MSE	9	Mod. Amino Acid	SELENOMETHIONINE
3	NHE	1	Ligand/Ion	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	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 , SER A:280 , ASP A:310 , ASP A:311 , HOH A:601 , HOH A:680	BINDING SITE FOR RESIDUE GMP A 500
2	AC2	SOFTWARE	HIS A:161 , HIS A:164	BINDING SITE FOR RESIDUE NHE A 600

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

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

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

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

(no "Exon" information available for 2QVN)

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:360
 aligned with A5KE01_PLAVS | A5KE01 from UniProtKB/TrEMBL  Length:363

    Alignment length:360
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363
         A5KE01_PLAVS     4 LQEPIDFLKKEELKNIDLSQMSKKERYKIWKRIPKCELHCHLDLCFSADFFVSCIRKYNLQPNLSDEEVLDYYLFAKGGKSLGEFVEKAIKVADIFHDYEVIEDLAKHAVFNKYKEGVVLMEFRYSPTFVAFKYNLDIELIHQAIVKGIKEVVELLDHKIHVALMCIGDTGHEAANIKASADFCLKHKADFVGFDHGGHEVDLKEYKEIFDYVRESGVPLSVHAGEDVTLPNLNTLYSAIQVLKVERIGHGIRVAESQELIDMVKEKNILLEVCPISNVLLKNAKSMDTHPIRQLYDAGVKVSVNSDDPGMFLTNINDDYEELYTHLNFTLEDFMKMNEWALEKSFMDSNIKDKIKNLYF 363
               SCOP domains d2qvna_ A: automated matches                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains -------------------------------A_deaminase-2qvnA01 A:35-361                                                                                                                                                                                                                                                                                                           -- Pfam domains
         Sec.struct. author ...........hhhhhhhhhhhhhhhhhhhhhh.eeeeeee.hhh.hhhhhhhhhhhh......hhhhhhhhhh......hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhheeeeeeeehhhhhhh....hhhhhhhhhhhhhhhhhhhh....eeeeeeeeee.....hhhhhhhhhhhh...eeeeeeee...hhhhhhhhhhhhhhh....eeee........hhhhhhhhhh....eeee.hhhhhhhhhhhhhhhh..eeeehhhhhhhh.........hhhhhhhh..eeee...hhhhhh.hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2qvn A   4 LQEPIDFLKKEELKNIDLSQmSKKERYKIWKRIPKCELHCHLDLCFSADFFVSCIRKYNLQPNLSDEEVLDYYLFAKGGKSLGEFVEKAIKVADIFHDYEVIEDLAKHAVFNKYKEGVVLmEFRYSPTFVAFKYNLDIELIHQAIVKGIKEVVELLDHKIHVALmCIGDTGHEAANIKASADFCLKHKADFVGFDHGGHEVDLKEYKEIFDYVRESGVPLSVHAGEDVTLPNLNTLYSAIQVLKVERIGHGIRVAESQELIDmVKEKNILLEVCPISNVLLKNAKSmDTHPIRQLYDAGVKVSVNSDDPGmFLTNINDDYEELYTHLNFTLEDFmKmNEWALEKSFmDSNIKDKIKNLYF 363
                                    13        23|       33        43        53        63        73        83        93       103       113       123|      133       143       153       163    |  173       183       193       203       213       223       233       243       253       263  |    273       283      |293       303       313|      323       333    | |343      |353       363
                                               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: 126793] (1)

d2qvna_

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

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Amidohydrolase (126)

Family: A_deaminase (23)

Plasmodium vivax (strain Salvador I) (3)

A_deaminase-2qvnA01

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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	Ligands, Modified Residues, Ions
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		MSE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2qvn)

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	2qvn
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	3.5.4.4
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UniProtKB/TrEMBL
	A5KE01_PLAVS \| A5KE01	:	2pgf 2pgr 3ewc 3ewd

2pgf	THE SAME PROTEIN IN COMPLEX WITH ADENOSINE
2pgr	THE SAME PROTEIN IN COMPLEX WITH 2'-DEOXYCOFORMYCIN (PENTOSTATIN)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 11)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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