2H8I - JenaLib

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

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF THE BOTHROPSTOXIN-I COMPLEXED WITH POLYETHYLENE GLYCOL

Authors :   M. T. Murakami, R. K. Arni

Date :   07 Jun 06 (Deposition) - 19 Jun 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Lys49-Pla2S, Myotoxicity, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. T. Murakami, M. M. Vicotia, J. R. B. Abrego, M. R. Lourenzoni, A. C. O. Cintra, E. Z. Arruda, M. A. Tomaz, P. A. Melo, R. K. Arni
Interfacial Surface Charge And Free Accessibility To The Pla2-Active Site-Like Region Are Essential Requirements For The Activity Of Lys49 Pla2 Homologues
Toxicon V. 49 378 2007
PubMed-ID: 17157889 | Reference-DOI: 10.1016/J.TOXICON.2006.10.011

Molecule 1 - PHOSPHOLIPASE A2 HOMOLOG 1
	Chains	:	A, B
	Organism Common	:	JARARACUSSU
	Organism Scientific	:	BOTHROPS JARARACUSSU
	Organism Taxid	:	8726
	Other Details	:	VENOM GLAND
	Synonym	:	BOTHROPSTOXIN I, BTHTX-I, BTXTXI

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	PEG	2	Ligand/Ion	DI(HYDROXYETHYL)ETHER

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR B:21 , CYS B:28 , GLY B:29 , HOH B:246	BINDING SITE FOR RESIDUE PEG B 201
2	AC2	SOFTWARE	LEU A:5 , TYR A:21 , GLY A:22 , ASN A:27 , CYS A:28 , GLY A:29 , VAL A:30 , CYS A:44 , HIS A:47 , HOH A:243 , LEU B:31	BINDING SITE FOR RESIDUE PEG A 202

Asymmetric/Biological Unit

No.	Residues
1	A:26	-	A:115
2	A:28	-	A:44
3	A:43	-	A:95
4	A:49	-	A:121
5	A:50	-	A:88
6	A:57	-	A:81
7	A:75	-	A:86
8	B:26	-	B:115
9	B:28	-	B:44
10	B:43	-	B:95
11	B:49	-	B:121
12	B:50	-	B:88
13	B:57	-	B:81
14	B:75	-	B:86

(no "Cis Peptide Bond" information available for 2H8I)

Asymmetric/Biological Unit (3, 6)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_PA2B1_BOTJR_001 *	F	19	L	PA2B1_BOTJR	---	---	A/B	F	3	L
2	UniProt	VAR_PA2B1_BOTJR_002 *	Y	37	H	PA2B1_BOTJR	---	---	A/B	Y	21	H
3	UniProt	VAR_PA2B1_BOTJR_003 *	P	136	A	PA2B1_BOTJR	---	---	A/B	P	120	A
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA2B1_BOTJR	59-66	2	A:43-50 B:43-50
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2B1_BOTJR	101-111	2	A:85-95 B:85-95

(no "Exon" information available for 2H8I)

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:121
 aligned with PA2B1_BOTJR | Q90249 from UniProtKB/Swiss-Prot  Length:137

    Alignment length:121
                                    26        36        46        56        66        76        86        96       106       116       126       136 
          PA2B1_BOTJR    17 SLFELGKMILQETGKNPAKSYGAYGCNCGVLGRGKPKDATDRCCYVHKCCYKKLTGCDPKKDRYSYSWKDKTIVCGENNPCLKELCECDKAVAICLRENLGTYNKKYRYHLKPFCKKADPC 137
               SCOP domains d2h8ia_ A: automated matches                                                                                              SCOP domains
               CATH domains 2h8iA00 A:1-121 Phospholipase A2                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhhhee...ee........hhhhhhhhhhhhhhh.............eeee..eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) --L-----------------H--------------------------------------------------------------------------------------------------A- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS ----------------------------------PA2_ASP    -------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 2h8i A   1 SLFELGKMILQETGKNPAKSYGAYGCNCGVLGRGKPKDATDRCCYVHKCCYKKLTGCNPKKDRYSYSWKDKTIVCGENNPCLKELCECDKAVAICLRENLGTYNKKYRYHLKPFCKKADPC 121
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain B from PDB  Type:PROTEIN  Length:121
 aligned with PA2B1_BOTJR | Q90249 from UniProtKB/Swiss-Prot  Length:137

    Alignment length:121
                                    26        36        46        56        66        76        86        96       106       116       126       136 
          PA2B1_BOTJR    17 SLFELGKMILQETGKNPAKSYGAYGCNCGVLGRGKPKDATDRCCYVHKCCYKKLTGCDPKKDRYSYSWKDKTIVCGENNPCLKELCECDKAVAICLRENLGTYNKKYRYHLKPFCKKADPC 137
               SCOP domains d2h8ib_ B: automated matches                                                                                              SCOP domains
               CATH domains 2h8iB00 B:1-121 Phospholipase A2                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhhh...............hhhhhhhhhhhhhhhh............eeee..eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh...... Sec.struct. author
                 SAPs(SNPs) --L-----------------H--------------------------------------------------------------------------------------------------A- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS ----------------------------------PA2_ASP    -------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 2h8i B   1 SLFELGKMILQETGKNPAKSYGAYGCNCGVLGRGKPKDATDRCCYVHKCCYKKLTGCNPKKDRYSYSWKDKTIVCGENNPCLKELCECDKAVAICLRENLGTYNKKYRYHLKPFCKKADPC 121
                                    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 '\|'

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: automated matches (75)

Jararacussu (Bothrops jararacussu) [TaxId: 8726] (7)

1a	d2h8ia_	A:
1b	d2h8ib_	B:

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)

Jararacussu (Bothrops jararacussu) (9)

1a	2h8iA00	A:1-121
1b	2h8iB00	B:1-121

(no "Pfam Domain" information available for 2H8I)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (PA2B1_BOTJR | Q90249)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0004623	phospholipase A2 activity	Catalysis of the reaction: phosphatidylcholine + H2O = 1-acylglycerophosphocholine + a carboxylate.
biological process
	GO:0042742	defense response to bacterium	Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
	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.
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
		PEG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

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

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2h8i)

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
	2h8i
		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
	PA2B1_BOTJR \| Q90249
		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)
	(no 'Enzyme Classificator' available)
		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
	PA2B1_BOTJR \| Q90249
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	PA2B1_BOTJR \| Q90249	:	3cxi 3hzd 3hzw 3i03 3i3h 3i3i 3iq3 4k06 4k09 4wtb

(no "Related Entries Specified in the PDB File" available for 2H8I)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (14, 14)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (3, 6)

PROSITE Motifs (2, 4)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (0, 0)

Gene Ontology (5, 5)

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