1VL9 - JenaLib

Asym./Biol. Unit

Asym./Biol. Unit - sites

collapse

expand

Asym./Biol. Unit (Jmol Viewer)

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

Description

Title :   ATOMIC RESOLUTION (0.97A) STRUCTURE OF THE TRIPLE MUTANT (K53,56,121M) OF BOVINE PANCREATIC PHOSPHOLIPASE A2

Authors :   K. Sekar, D. Velmurugan, V. Rajakannan, D. Gayathri, M. -J. Poi, M. - D. Tsai, M. Dauter, Z. Dauter

Date :   15 Jul 04 (Deposition) - 19 Oct 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   0.97

Chains :   Asym./Biol. Unit : A

Keywords :   Alpha Helix, Beta Sheet, Triple Mutant, Calcium Ion, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Sekar, V. Rajakannan, D. Gayathri, D. Velmurugan, M. J. Poi, M. Dauter, Z. Dauter, M. D. Tsai
Atomic Resolution (0. 97 A) Structure Of The Triple Mutant (K53, 56, 121M) Of Bovine Pancreatic Phospholipase A2.
Acta Crystallogr. , Sect. F V. 61 3 2005
PubMed-ID: 16508077 | Reference-DOI: 10.1107/S1744309104021748
(for further references see the PDB file header)

Compounds

Molecule 1 - PHOSPHOLIPASE A2
	Chains	:	A
	EC Number	:	3.1.1.4
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	PLA2G1B
	Mutation	:	YES
	Organism Common	:	CATTLE
	Organism Scientific	:	BOS TAURUS
	Organism Taxid	:	9913
	Synonym	:	PHOSPHATIDYLCHOLINE 2-ACYLHYDROLASE, GROUP IB PHOSPHOLIPASE A2

Structural Features

Chains, Units

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (4, 9)

Asymmetric/Biological Unit (4, 9)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION
2	CL	1	Ligand/Ion	CHLORIDE ION
3	MPD	3	Ligand/Ion	(4S)-2-METHYL-2,4-PENTANEDIOL
4	MRD	3	Ligand/Ion	(4R)-2-METHYLPENTANE-2,4-DIOL

Sites (9, 9)

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:28 , GLY A:30 , GLY A:32 , ASP A:49 , HOH A:204 , HOH A:206	BINDING SITE FOR RESIDUE CA A 124
2	AC2	SOFTWARE	ASN A:71 , ASN A:72 , GLU A:92 , HOH A:207 , HOH A:212 , HOH A:431	BINDING SITE FOR RESIDUE CA A 125
3	AC3	SOFTWARE	LYS A:12 , GLU A:81 , ILE A:82 , ARG A:100 , ILE A:104 , HOH A:264	BINDING SITE FOR RESIDUE CL A 126
4	AC4	SOFTWARE	MET A:56 , TYR A:69 , HOH A:387 , HOH A:399 , MPD A:1602 , MPD A:1605	BINDING SITE FOR RESIDUE MRD A 1603
5	AC5	SOFTWARE	LEU A:2 , PRO A:18 , PHE A:22 , GLY A:30 , HOH A:206	BINDING SITE FOR RESIDUE MRD A 1604
6	AC6	SOFTWARE	SER A:15 , TYR A:111 , HOH A:438	BINDING SITE FOR RESIDUE MRD A 1606
7	AC7	SOFTWARE	ASN A:23 , ASN A:24 , GLY A:26 , CYS A:27 , CYS A:29 , GLY A:30 , LEU A:31 , GLY A:32 , LEU A:118 , HOH A:210 , HOH A:227 , HOH A:305 , HOH A:370 , HOH A:376 , HOH A:380 , HOH A:385	BINDING SITE FOR RESIDUE MPD A 1601
8	AC8	SOFTWARE	LEU A:31 , ASP A:49 , MET A:56 , TYR A:69 , HOH A:204 , MRD A:1603	BINDING SITE FOR RESIDUE MPD A 1602
9	AC9	SOFTWARE	LEU A:2 , LEU A:58 , PHE A:94 , HOH A:313 , HOH A:387 , MRD A:1603	BINDING SITE FOR RESIDUE MPD A 1605

SS Bonds (7, 7)

Asymmetric/Biological Unit

No.	Residues
1	A:11	-	A:77
2	A:27	-	A:123
3	A:29	-	A:45
4	A:44	-	A:105
5	A:51	-	A:98
6	A:61	-	A:91
7	A:84	-	A:96

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 1VL9)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 1VL9)

PROSITE Motifs (2, 2)

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA21B_BOVIN	66-73	1	A:44-51
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA21B_BOVIN	117-127	1	A:95-105

Exons (0, 0)

(no "Exon" information available for 1VL9)

Sequences/Alignments

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:123
 aligned with PA21B_BOVIN | P00593 from UniProtKB/Swiss-Prot  Length:145

    Alignment length:123
                                    32        42        52        62        72        82        92       102       112       122       132       142   
          PA21B_BOVIN    23 ALWQFNGMIKCKIPSSEPLLDFNNYGCYCGLGGSGTPVDDLDRCCQTHDNCYKQAKKLDSCKVLVDNPYTNNYSYSCSNNEITCSSENNACEAFICNCDRNAAICFSKVPYNKEHKNLDKKNC 145
               SCOP domains d1vl9a_ A: Phospholipase A2                                                                                                 SCOP domains
               CATH domains 1vl9A00 A:1-123 Phospholipase A2                                                                                            CATH domains
               Pfam domains Phospholip_A2_1-1vl9A01 A:1-123                                                                                             Pfam domains
         Sec.struct. author hhhhhhhhhhhhh...hhhhhh................hhhhhhhhhhhhhhhhhhhh................eeee..eeee....hhhhhhhhhhhhhhhhhhhhh..hhhhh..hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------PA2_HIS -------------------------------------------PA2_ASP    ------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vl9 A   1 ALWQFNGMIKCKIPSSEPLLDFNNYGCYCGLGGSGTPVDDLDRCCQTHDNCYMQAMKLDSCKVLVDNPYTNNYSYSCSNNEITCSSENNACEAFICNCDRNAAICFSKVPYNKEHKNLDKMNC 123
                                    10        20        30        40        50        60        70        80        90       100       110       120

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 (1, 1)

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Phospholipase A2, PLA2 (282)

Superfamily: Phospholipase A2, PLA2 (282)

Family: Vertebrate phospholipase A2 (271)

Protein domain: Phospholipase A2 (72)

Cow (Bos taurus), pancreas [TaxId: 9913] (32)

d1vl9a_

CATH Domains (1, 1)

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Up-down Bundle (3216)

Topology: Phospholipase A2 (241)

Homologous Superfamily: Phospholipase A2 (241)

Cattle (Bos taurus) (29)

1vl9A00

A:1-123

Pfam Domains (1, 1)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Phospholip_A2_1] (33)

Family: Phospholip_A2_1 (33)

Bos taurus (Bovine) (10)

Phospholip_A2_1-1vl9A01

A:1-123

Gene Ontology (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (PA21B_BOVIN | P00593)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004623	phospholipase A2 activity	Catalysis of the reaction: phosphatidylcholine + H2O = 1-acylglycerophosphocholine + a carboxylate.
biological process
	GO:0016042	lipid catabolic process	The chemical reactions and pathways resulting in the breakdown of lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
	GO:0006629	lipid metabolic process	The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Visualization

Interactive Views

Asymmetric/Biological 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
		CA	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MPD	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MRD	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1vl9)

Still Images

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites 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
	1vl9
		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
	PA21B_BOVIN \| P00593
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	3.1.1.4
		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
	PA21B_BOVIN \| P00593
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	PA21B_BOVIN \| P00593	:	1bp2 1bpq 1bvm 1c74 1ceh 1fdk 1g4i 1gh4 1irb 1kvw 1kvx 1kvy 1mks 1mkt 1mku 1mkv 1o2e 1o3w 1une 1vkq 2b96 2bax 2bch 2bd1 2bp2 2bpp 2zp3 2zp4 2zp5 3bp2 4bp2

Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1VL9)