1OWS - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A C49 PHOSPHOLIPASE A2 FROM INDIAN COBRA REVEALS CARBOHYDRATE BINDING IN THE HYDROPHOBIC CHANNEL

Authors :   T. Jabeen, J. Jasti, N. Singh, R. K. Singh, S. Sharma, P. Kaur, T. P. Singh

Date :   30 Mar 03 (Deposition) - 20 May 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: A,B  (2x)
Biol. Unit 3: A,B  (2x)

Keywords :   Phospholipase, Enzyme, Phospholipids, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Jabeen, J. Jasti, N. Singh, R. K. Singh, S. Sharma, P. Kaur, T. P. Sing
Crystal Structure Of A C49 Phospholipase A2 From Indian Cobra Reveals Carbohydrate Binding In The Hydrophobic Channel
To Be Published
PubMed: search

Molecule 1 - PHOSPHOLIPASE A2
	Chains	:	A
	EC Number	:	3.1.1.4
	Organism Common	:	INDIAN COBRA
	Organism Scientific	:	NAJA NAJA
	Organism Taxid	:	35670
	Secretion	:	VENOM

Molecule 2 - PHOSPHOLIPASE A2
	Chains	:	B
	EC Number	:	3.1.1.4
	Organism Common	:	INDIAN COBRA
	Organism Scientific	:	NAJA NAJA
	Organism Taxid	:	35670
	Secretion	:	VENOM

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (2x)	:	A	B
Biological Unit 3 (2x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 3)

No.	Name	Count	Type	Full Name
1	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
2	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
2	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
2	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR A:2 , PHE A:5 , TRP A:19 , PHE A:22 , TYR A:28 , CYS A:29 , GLY A:30 , CYS A:32 , HIS A:48 , LYS A:64 , HOH A:2082	BINDING SITE FOR RESIDUE NAG A 2001
2	AC2	SOFTWARE	ASP A:24 , ASN A:112 , HOH A:2002 , ASP B:24 , ASN B:112 , HOH B:200	BINDING SITE FOR RESIDUE ZN A 1001
3	AC3	SOFTWARE	GLN A:71 , ASN A:120	BINDING SITE FOR RESIDUE ZN A 1002

Asymmetric Unit

No.	Residues
1	A:11	-	A:72
2	A:27	-	A:119
3	A:29	-	A:45
4	A:32	-	A:49
5	A:44	-	A:100
6	A:51	-	A:93
7	A:61	-	A:86
8	A:79	-	A:91
9	B:11	-	B:72
10	B:27	-	B:119
11	B:29	-	B:45
12	B:44	-	B:100
13	B:51	-	B:93
14	B:61	-	B:86
15	B:79	-	B:91

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

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

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA2A2_NAJNA	43-50	2	A:44-51 B:44-51
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2A2_NAJNA	89-99	2	A:91-100 B:91-100

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA2A2_NAJNA	43-50	2	A:44-51 B:44-51
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2A2_NAJNA	89-99	2	A:91-100 B:91-100

Biological Unit 2 (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA2A2_NAJNA	43-50	4	A:44-51 B:44-51
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2A2_NAJNA	89-99	4	A:91-100 B:91-100

Biological Unit 3 (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA2A2_NAJNA	43-50	4	A:44-51 B:44-51
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2A2_NAJNA	89-99	4	A:91-100 B:91-100

(no "Exon" information available for 1OWS)

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:118
 aligned with PA2A2_NAJNA | P15445 from UniProtKB/Swiss-Prot  Length:119

    Alignment length:119
                                    10        20        30        40        50        60        70        80        90       100       110         
          PA2A2_NAJNA     1 NLYQFKNMIKCTVPSRSWWDFADYGCYCGRGGSGTPVDDLDRCCQVHDNCYNEAEKISGCWPYFKTYSYECSQGTLTCKGDNNACAASVCDCDRLAAICFAGAPYNDNNYNIDLKARCQ 119
               SCOP domains d1owsa_ A: Snake phospholipas e A2                                                                                      SCOP domains
               CATH domains 1owsA00 A:1-120 Phospholipase  A2                                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh...hhhhhh.......-.......hhhhhhhhhhhhhhhhhh.............eeee..eeee....hhhhhhhhhhhhhhhhhhhhh..hhhhh..hhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS --------------------------------------PA2_ASP    -------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 1ows A   1 NTYQFRNMIECTVPSRSWWDFADYGCYCG-CGSGTPTDDLDRCCQVHCNCYRQAGEISGCRPKFKTYTYQCSGGTLTCKGNNNACAASSCDCDRLAAICFAGAPYNDNNYNIDLKARCN 120
                                    10    ||  21        |-|       41        51        61        71        81        91       101       111         
                                         15|           30 |                                                                                        
                                          17             32

Chain B from PDB  Type:PROTEIN  Length:118
 aligned with PA2A2_NAJNA | P15445 from UniProtKB/Swiss-Prot  Length:119

    Alignment length:119
                                    10        20        30        40        50        60        70        80        90       100       110         
          PA2A2_NAJNA     1 NLYQFKNMIKCTVPSRSWWDFADYGCYCGRGGSGTPVDDLDRCCQVHDNCYNEAEKISGCWPYFKTYSYECSQGTLTCKGDNNACAASVCDCDRLAAICFAGAPYNDNNYNIDLKARCQ 119
               SCOP domains d1owsb_ B: Snake phospholipase  A2                                                                                      SCOP domains
               CATH domains 1owsB00 B:1-120 Phospholipase  A2                                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh....hhhhhh.......-......hhhhhhhhhhhhhhhhhhh............eeee..eeee....hhhhhhhhhhhhhhhhhhhhh..hhhhh..hhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS --------------------------------------PA2_ASP    -------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 1ows B   1 NIKQFNNMIECTVPARSWWDFADYGCYCGS-GSGSPTDDLDRCCQTHDNCYGAGGGSTGCAPKSRTYTYQCSQGTLTCSGENSACAATTCDCDRLAAICFAGAPYNDTNYNIDLKSRCQ 120
                                    10    ||  21        31 |      41        51        61        71        81        91       101       111         
                                         15|            31 |                                                                                       
                                          17              33

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 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: Snake phospholipase A2 (124)

Indian cobra (Naja naja), a C49 isoform 2 [TaxId: 35670] (1)

d1owsa_

Indian cobra (Naja naja), isoform 3 [TaxId: 35670] (1)

d1owsb_

Asymmetric 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)

Indian cobra (Naja naja) (5)

1a	1owsA00	A:1-120
1b	1owsB00	B:1-120

(no "Pfam Domain" information available for 1OWS)

Asymmetric Unit(hide GO term definitions)

Chain A,B (PA2A2_NAJNA | P15445)

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.

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
		NAG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ZN	[ 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 1ows)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]

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 \| Biol. Unit 3 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)

Access by PDB/NDB ID
	1ows
		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
	PA2A2_NAJNA \| P15445
		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

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
	PA2A2_NAJNA \| P15445
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	PA2A2_NAJNA \| P15445	:	1a3d 1a3f 1psh 2wq5

1lff	CRYSTAL STRUCTURE OF AN ACIDIC PHOSPHOLIPASE A2 FROM NAJA NAJA SAGITTIFERA AT 1.5 A RESOLUTION
1lfj	X-RAY CRYSTAL STRUCTURE OF A COMPLEX FORMED BETWEEN TWO HOMOLOGOUS ISOFORMS OF PHOSPHOLIPASE A2 FROM NAJA NAJA SAGITTIFERA: PRINCIPLE OF MOLECULAR ASSOCIATION AND INACTIVATION
1ln8	CRYSTAL STRUCTURE OF A NEW ISOFORM OF PHOSPHOLIPASE A2 FROM NAJA NAJA SAGITTIFERA AT 1.6 A RESOLUTION
1mh2	CRYSTAL STRUCTURE OF A ZINC CONTAINING DIMER OF PHOSPHOLIPASE A2 FROM THE VENOM OF INDIAN COBRA (NAJA NAJA SAGITTIFERA)
1mh7	CRYSTAL STRUCTURE OF A CALCIUM-FREE ISOFORM OF PHOSPHOLIPASE A2 FROM NAJA NAJA SAGITTIFERA AT 2.0 A RESOLUTION
1mh8	CRYSTAL STRUCTURE OF A PHOPHOLIPASE A2 MONOMER WITH ISOLEUCINE AT SECOND POSITION

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 3)

Sites (3, 3)

SS Bonds (15, 15)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (7, 7)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File