4WIN - JenaLib

Title :   CRYSTAL STRUCTURE OF THE GATASE DOMAIN FROM PLASMODIUM FALCIPARUM GMP SYNTHETASE

Authors :   L. Ballut, S. Violot, R. Haser, N. Aghajari

Date :   26 Sep 14 (Deposition) - 02 Dec 15 (Release) - 09 Dec 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Gmp Synthetase, Plasmodium Falciparum, Purine Salvage Pathway, Glutamine Amidotransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   L. Ballut, S. Violot, S. Shivakumaraswamy, L. P. Thota, M. Sathya, J. Kunala, B. W. Dijkstra, R. Terreux, R. Haser, H. Balaram, N. Aghajar
Active Site Coupling In Plasmodium Falciparum Gmp Synthetas Is Triggered By Domain Rotation.
Nat Commun V. 6 8930 2015
PubMed-ID: 26592566 | Reference-DOI: 10.1038/NCOMMS9930

Compounds

Molecule 1 - GMP SYNTHETASE
	Chains	:	A, B
	EC Number	:	6.3.5.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-21B(+)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PF10_0123
	Organism Scientific	:	PLASMODIUM FALCIPARUM
	Organism Taxid	:	36329
	Strain	:	ISOLATE 3D7

Structural Features

Chains, Units

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (1, 3)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	NO3	3	Ligand/Ion	NITRATE ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	NO3	2	Ligand/Ion	NITRATE ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	NO3	1	Ligand/Ion	NITRATE ION

Sites (3, 3)

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:13 , PHE A:19 , THR A:35 , ASN B:13 , PHE B:19 , THR B:35 , LYS B:36 , ASP B:37	binding site for residue NO3 A 1001
2	AC2	SOFTWARE	SER A:16 , GLN A:17 , TYR A:18 , GLY A:57 , GLY A:58 , HIS A:208 , TYR B:60	binding site for residue NO3 A 1002
3	AC3	SOFTWARE	TYR A:60 , SER B:16 , GLN B:17 , GLY B:58 , HIS B:208	binding site for residue NO3 B 301

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Asymmetric 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:228
                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee....hhhhhhhhhhhh...eeeee...hhhhhh...eeeeee...............hhhhhhhhhhh...eeeehhhhhhhhhhh..eeeeeeeeeeeeeeeee....hhhhh.hhhhh....hhhhhhhhh......hhhhh.....eeeeeeeeeeeeee.....eeeeee..eeeeeeee....eeee..........hhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4win A   6 YDKILVLNFGSQYFHLIVKRLNNIKIFSETKDYGVELKDIKDMNIKGVILSGGPYSVTEAGSPHLKKEVFEYFLEKKIPIFGICYGMQEIAVQMNGEVKKSKTSEYGCTDVNILRNDNINNITYCRNFGDSSSAMDLYSNYKLMNETCCLFENIKSDITTVWMNHNDEVTKIPENFYLVSSSENCLICSIYNKEYNIYGVQYHPEVYESLDGELMFYNFAYNICKCKK 233
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225

Chain B from PDB  Type:PROTEIN  Length:228
                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee....hhhhhhhhhhhh..eeeeee...hhhhh....eeeeee...............hhhhhhhhhhh...eeeehhhhhhhhhhh..eeeeeeeeeeeeeeeee.hhhhhhhh.hhhhhh...hhhhhhhhh......hhhhh.....eeeeeeeeeeeeee.....eeeee.......eeee....eeee..........hhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4win B   6 YDKILVLNFGSQYFHLIVKRLNNIKIFSETKDYGVELKDIKDMNIKGVILSGGPYSVTEAGSPHLKKEVFEYFLEKKIPIFGICYGMQEIAVQMNGEVKKSKTSEYGCTDVNILRNDNINNITYCRNFGDSSSAMDLYSNYKLMNETCCLFENIKSDITTVWMNHNDEVTKIPENFYLVSSSENCLICSIYNKEYNIYGVQYHPEVYESLDGELMFYNFAYNICKCKK 233
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225

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 '\|'

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (8, 8)

Visualization

Interactive Views

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		NO3	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4win)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Still Images

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	4win
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	Q8IJR9_PLAF7 \| Q8IJR9
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

Access by Enzyme Classificator (EC Number)
	6.3.5.2
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Analysis Tools

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	Q8IJR9_PLAF7 \| Q8IJR9
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description