1B4W - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   BASIC PHOSPHOLIPASE A2 FROM AGKISTRODON HALYS PALLAS-IMPLICATIONS FOR ITS ASSOCIATION AND ANTICOAGULANT ACTIVITIES BY X-RAY CRYSTALLOGRAPHY

Authors :   K. H. Zhao, Z. J. Lin

Date :   30 Dec 98 (Deposition) - 12 Jan 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

Chains :   Asym./Biol. Unit : A,B,C,D

Keywords :   Basic Phospholipase A2, Agkistrodon Halys Pallas, Dimer, Anticoagulant Activity, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Zhao, Y. Zhou, Z. Lin
Structure Of Basic Phospholipase A2 From Agkistrodon Halys Pallas: Implications For Its Association, Hemolytic And Anticoagulant Activities.
Toxicon V. 38 901 2000
PubMed-ID: 10728829 | Reference-DOI: 10.1016/S0041-0101(99)00193-2
(for further references see the PDB file header)

Molecule 1 - PROTEIN (PHOSPHOLIPASE A2)
	Cellular Location	:	EXTRACELLULAR
	Chains	:	A, B, C, D
	EC Number	:	3.1.1.4
	Organism Common	:	HALYS VIPER
	Organism Scientific	:	GLOYDIUS HALYS
	Organism Taxid	:	8714
	Secretion	:	YES
	Synonym	:	PLA2

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	BOG	2	Ligand/Ion	B-OCTYLGLUCOSIDE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	AUTHOR	HIS A:48 , ASP A:99	ACTIVE SITE 1
2	AC2	AUTHOR	HIS B:48 , ASP B:99	ACTIVE SITE 2
3	AC3	AUTHOR	HIS C:48 , ASP C:99	ACTIVE SITE 3
4	AC4	AUTHOR	HIS D:48 , ASP D:99	ACTIVE SITE 4
5	AC5	SOFTWARE	ALA A:23 , PHE A:24 , SER A:31 , PHE C:24 , ILE D:124	BINDING SITE FOR RESIDUE BOG A 200
6	AC6	SOFTWARE	TYR D:22 , CYS D:29 , HIS D:48 , TYR D:52 , HOH D:317	BINDING SITE FOR RESIDUE BOG D 300

Asymmetric/Biological Unit

No.	Residues
1	A:27	-	A:126
2	A:29	-	A:45
3	A:44	-	A:105
4	A:50	-	A:133
5	A:51	-	A:98
6	A:61	-	A:91
7	A:84	-	A:96
8	B:27	-	B:126
9	B:29	-	B:45
10	B:44	-	B:105
11	B:50	-	B:133
12	B:51	-	B:98
13	B:61	-	B:91
14	B:84	-	B:96
15	C:27	-	C:126
16	C:29	-	C:45
17	C:44	-	C:105
18	C:50	-	C:133
19	C:51	-	C:98
20	C:61	-	C:91
21	C:84	-	C:96
22	D:27	-	D:126
23	D:29	-	D:45
24	D:44	-	D:105
25	D:50	-	D:133
26	D:51	-	D:98
27	D:61	-	D:91
28	D:84	-	D:96

(no "Cis Peptide Bond" information available for 1B4W)

(no "SAP(SNP)/Variant" information available for 1B4W)

Asymmetric/Biological Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA2BB_GLOHA	59-66	4	A:44-51 B:44-51 C:44-51 D:44-51
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2BB_GLOHA	101-111	4	A:95-105 B:95-105 C:95-105 D:95-105

(no "Exon" information available for 1B4W)

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:122
 aligned with PA2BB_GLOHA | O42187 from UniProtKB/Swiss-Prot  Length:138

    Alignment length:122
                                    26        36        46        56        66        76        86        96       106       116       126       136  
          PA2BB_GLOHA    17 SLLQFRKMIKKMTGKEPVVSYAFYGCYCGSGGRGKPKDATDRCCFVHDCCYEKLTGCDPKWDDYTYSWKNGTIVCGGDDPCKKEVCECDKAAAICFRDNLKTYKKRYMTYPNILCSSKSEKC 138
               SCOP domains d1b4wa_ A: Snake phospholipase A2                                                                                          SCOP domains
               CATH domains 1b4wA00 A:1-133 Phospholipase A2                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh...hhhh..................hhhhhhhhhhhhhhh............ee.hhh..ee....hhhhhhhhhhhhhhhhhhh.hhh..hhh....hhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS ----------------------------------PA2_ASP    --------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 1b4w A   1 HLLQFRKMIKKMTGKEPVVSYAFYGCYCGSGGRGKPKDATDRCCFVHDCCYEKVTGCDPKWDDYTYSWKNGTIVCGGDDPCKKEVCECDKAAAICFRDNLKTYKKRYMAYPDILCSSKSEKC 133
                                    10   ||   21        31        41        51    ||||69        79      ||90       100       110       120 ||    131  
                                        14|                                      56|||                 86|                               122|         
                                         16                                       59||                  88                                124         
                                                                                   61|                                                                
                                                                                    67

Chain B from PDB  Type:PROTEIN  Length:122
 aligned with PA2BB_GLOHA | O42187 from UniProtKB/Swiss-Prot  Length:138

    Alignment length:122
                                    26        36        46        56        66        76        86        96       106       116       126       136  
          PA2BB_GLOHA    17 SLLQFRKMIKKMTGKEPVVSYAFYGCYCGSGGRGKPKDATDRCCFVHDCCYEKLTGCDPKWDDYTYSWKNGTIVCGGDDPCKKEVCECDKAAAICFRDNLKTYKKRYMTYPNILCSSKSEKC 138
               SCOP domains d1b4wb_ B: Snake phospholipase A2                                                                                          SCOP domains
               CATH domains 1b4wB00 B:1-133 Phospholipase A2                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh...hhhh..................hhhhhhhhhhhhhhh............ee.hhh..ee....hhhhhhhhhhhhhhhhhhh.hhh..hhh....hhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS ----------------------------------PA2_ASP    --------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 1b4w B   1 HLLQFRKMIKKMTGKEPVVSYAFYGCYCGSGGRGKPKDATDRCCFVHDCCYEKVTGCDPKWDDYTYSWKNGTIVCGGDDPCKKEVCECDKAAAICFRDNLKTYKKRYMAYPDILCSSKSEKC 133
                                    10   ||   21        31        41        51    ||||69        79      ||90       100       110       120 ||    131  
                                        14|                                      56|||                 86|                               122|         
                                         16                                       59||                  88                                124         
                                                                                   61|                                                                
                                                                                    67

Chain C from PDB  Type:PROTEIN  Length:122
 aligned with PA2BB_GLOHA | O42187 from UniProtKB/Swiss-Prot  Length:138

    Alignment length:122
                                    26        36        46        56        66        76        86        96       106       116       126       136  
          PA2BB_GLOHA    17 SLLQFRKMIKKMTGKEPVVSYAFYGCYCGSGGRGKPKDATDRCCFVHDCCYEKLTGCDPKWDDYTYSWKNGTIVCGGDDPCKKEVCECDKAAAICFRDNLKTYKKRYMTYPNILCSSKSEKC 138
               SCOP domains d1b4wc_ C: Snake phospholipase A2                                                                                          SCOP domains
               CATH domains 1b4wC00 C:1-133 Phospholipase A2                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh...hhhh..................hhhhhhhhhhhhhhh............ee.hhh..ee....hhhhhhhhhhhhhhhhhhh.hhh..hhh....hhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS ----------------------------------PA2_ASP    --------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 1b4w C   1 HLLQFRKMIKKMTGKEPVVSYAFYGCYCGSGGRGKPKDATDRCCFVHDCCYEKVTGCDPKWDDYTYSWKNGTIVCGGDDPCKKEVCECDKAAAICFRDNLKTYKKRYMAYPDILCSSKSEKC 133
                                    10   ||   21        31        41        51    ||||69        79      ||90       100       110       120 ||    131  
                                        14|                                      56|||                 86|                               122|         
                                         16                                       59||                  88                                124         
                                                                                   61|                                                                
                                                                                    67

Chain D from PDB  Type:PROTEIN  Length:122
 aligned with PA2BB_GLOHA | O42187 from UniProtKB/Swiss-Prot  Length:138

    Alignment length:122
                                    26        36        46        56        66        76        86        96       106       116       126       136  
          PA2BB_GLOHA    17 SLLQFRKMIKKMTGKEPVVSYAFYGCYCGSGGRGKPKDATDRCCFVHDCCYEKLTGCDPKWDDYTYSWKNGTIVCGGDDPCKKEVCECDKAAAICFRDNLKTYKKRYMTYPNILCSSKSEKC 138
               SCOP domains d1b4wd_ D: Snake phospholipase A2                                                                                          SCOP domains
               CATH domains 1b4wD00 D:1-133 Phospholipase A2                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh...hhhh..................hhhhhhhhhhhhhhh............ee.hhh..ee....hhhhhhhhhhhhhhhhhhh.hhh..hhh....hhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS ----------------------------------PA2_ASP    --------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 1b4w D   1 HLLQFRKMIKKMTGKEPVVSYAFYGCYCGSGGRGKPKDATDRCCFVHDCCYEKVTGCDPKWDDYTYSWKNGTIVCGGDDPCKKEVCECDKAAAICFRDNLKTYKKRYMAYPDILCSSKSEKC 133
                                    10   ||   21        31        41        51    ||||69        79      ||90       100       110       120 ||    131  
                                        14|                                      56|||                 86|                               122|         
                                         16                                       59||                  88                                124         
                                                                                   61|                                                                
                                                                                    67

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: 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)

Halys viper (Agkistrodon halys) [TaxId: 8714] (9)

1a	d1b4wa_	A:
1b	d1b4wb_	B:
1c	d1b4wc_	C:
1d	d1b4wd_	D:

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)

Halys viper (Gloydius halys) (9)

1a	1b4wA00	A:1-133
1b	1b4wB00	B:1-133
1c	1b4wC00	C:1-133
1d	1b4wD00	D:1-133

(no "Pfam Domain" information available for 1B4W)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (PA2BB_GLOHA | O42187)

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/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
		BOG	[ 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 ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1b4w)

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)

Access by PDB/NDB ID
	1b4w
		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
	PA2BB_GLOHA \| O42187
		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
	PA2BB_GLOHA \| O42187
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	PA2BB_GLOHA \| O42187	:	1c1j 1jia 4hg9

(no "Related Entries Specified in the PDB File" available for 1B4W)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (6, 6)

SS Bonds (28, 28)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 8)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (1, 4)

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