3MLM - JenaLib

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Title :   CRYSTAL STRUCTURE OF BN IV IN COMPLEX WITH MYRISTIC ACID: A LYS49 MYOTOXIC PHOSPHOLIPASE A2 FROM BOTHROPS NEUWIEDI VENOM

Authors :   P. Delatorre, B. A. M. Rocha, B. S. Cavada, M. H. Toyama, D. Toyama, C. A. A

Date :   17 Apr 10 (Deposition) - 18 May 11 (Release) - 18 May 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.21

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

Keywords :   Myotoxin, Phospholipase-Like Protein, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Delatorre, B. A. Rocha, T. Santi-Gadelha, C. A. Gadelha, M. H. Toyama, B. S. Cavada
Crystal Structure Of Bn Iv In Complex With Myristic Acid: A Lys49 Myotoxic Phospholipase A2 From Bothrops Neuwiedi Venom.
Biochimie V. 93 513 2011
PubMed-ID: 21108987 | Reference-DOI: 10.1016/J.BIOCHI.2010.11.003

Molecule 1 - BN-IV LYS-49 PHOSPHOLIPASE A2
	Chains	:	A, B
	EC Number	:	3.1.1.4
	Organism Common	:	NEUWIED'S LANCEHEAD
	Organism Scientific	:	BOTHROPS NEUWIEDI PAULOENSIS
	Organism Taxid	:	95649
	Other Details	:	TOXIN
	Secretion	:	VENOM
	Synonym	:	PHOSPHOLIPASE A2 HOMOLOG, PHOSPHOLIPASE A2 II

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	MYR	2	Ligand/Ion	MYRISTIC ACID
2	SO4	4	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	MYR	1	Ligand/Ion	MYRISTIC ACID
2	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	MYR	1	Ligand/Ion	MYRISTIC ACID
2	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:19 , THR A:55 , LYS A:105 , ARG A:108	BINDING SITE FOR RESIDUE SO4 A 123
2	AC2	SOFTWARE	GLY A:32 , ARG A:33 , LYS A:52	BINDING SITE FOR RESIDUE SO4 A 122
3	AC3	SOFTWARE	LEU A:5 , GLY A:6 , ILE A:9 , PRO A:17 , TYR A:21 , GLY A:29 , HOH A:162	BINDING SITE FOR RESIDUE MYR A 124
4	AC4	SOFTWARE	LYS B:19 , LYS B:105 , ARG B:108	BINDING SITE FOR RESIDUE SO4 B 123
5	AC5	SOFTWARE	GLY B:32 , ARG B:33 , LYS B:52	BINDING SITE FOR RESIDUE SO4 B 122
6	AC6	SOFTWARE	LEU B:5 , GLY B:6 , PRO B:17 , TYR B:21 , ASN B:27 , CYS B:28 , GLY B:29 , CYS B:44 , HIS B:47 , LYS B:48	BINDING SITE FOR RESIDUE MYR B 125

Asymmetric 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

Asymmetric Unit

No.	Residues
1	Cys A:28	-	Gly A:29

Asymmetric Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_PA2H_BOTPA_001 *	Q	34	G	PA2H_BOTPA	---	---	A/B	G	35	G
	* ID not provided by source

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

Biological Unit 1 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_PA2H_BOTPA_001 *	Q	34	G	PA2H_BOTPA	---	---	A	G	35	G
	* ID not provided by source

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

Biological Unit 2 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_PA2H_BOTPA_001 *	Q	34	G	PA2H_BOTPA	---	---	B	G	35	G
	* ID not provided by source

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

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA2H_BOTPA	42-49	2	A:43-50 B:43-50
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2H_BOTPA	84-94	2	A:85-95 B:85-95

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA2H_BOTPA	42-49	1	A:43-50 -
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2H_BOTPA	84-94	1	A:85-95 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PA2_HIS	PS00118	Phospholipase A2 histidine active site.	PA2H_BOTPA	42-49	1	- B:43-50
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2H_BOTPA	84-94	1	- B:85-95

(no "Exon" information available for 3MLM)

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:121
 aligned with PA2H_BOTPA | Q9IAT9 from UniProtKB/Swiss-Prot  Length:120

    Alignment length:121
                             1                                                                                                                       
                             |       9        19        29        39        49        59        69        79        89        99       109       119 
           PA2H_BOTPA     - -SFELGKMILQETGKNPAKSYGAYGCNCGVLGRGQPKDATDRCCYVHKCCYKKLTGCDPKKDRYSYSWKDKTIVCGENNPCLKELCECDKAVAICLRENLGTYNKKYRYHLKPFCKKADPC 120
               SCOP domains d3mlma_ A: Snake phospholipase A2                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhhh...............hhhhhhhhhhhhhhhh............eeee..eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------G-------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS ----------------------------------PA2_ASP    -------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mlm A   1 SLFELGKMILQETGKNPAKSYGAYGCNCGVLGRGGPKDATDRCCYVHKCCYKKITGCDPKKDRYSYSWKDKTIVCGENNPCLKELCECDKAVAICLRENLGTYNKKYRYHLKPFCKKADPC 121
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain B from PDB  Type:PROTEIN  Length:121
 aligned with PA2H_BOTPA | Q9IAT9 from UniProtKB/Swiss-Prot  Length:120

    Alignment length:121
                             1                                                                                                                       
                             |       9        19        29        39        49        59        69        79        89        99       109       119 
           PA2H_BOTPA     - -SFELGKMILQETGKNPAKSYGAYGCNCGVLGRGQPKDATDRCCYVHKCCYKKLTGCDPKKDRYSYSWKDKTIVCGENNPCLKELCECDKAVAICLRENLGTYNKKYRYHLKPFCKKADPC 120
               SCOP domains d3mlmb_ B: Snake phospholipase A2                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhhhee...ee........hhhhhhhhhhhhhhhh............eee....eee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------G-------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS ----------------------------------PA2_ASP    -------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mlm B   1 SLFELGKMILQETGKNPAKSYGAYGCNCGVLGRGGPKDATDRCCYVHKCCYKKITGCDPKKDRYSYSWKDKTIVCGENNPCLKELCECDKAVAICLRENLGTYNKKYRYHLKPFCKKADPC 121
                                    10        20        30        40        50        60        70        80        90       100       110       120

Legend:		→ Mismatch	(orange background)
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	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)

Neuwied's lancehead (Bothrops neuwiedi pauloensis), different isoforms [TaxId: 95649] (3)

1a	d3mlma_	A:
1b	d3mlmb_	B:

(no "CATH Domain" information available for 3MLM)

(no "Pfam Domain" information available for 3MLM)

Asymmetric Unit(hide GO term definitions)

Chain A,B (PA2H_BOTPA | Q9IAT9)

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.

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	Cis Peptide Bonds
		Cys A:28 - Gly A:29	[ RasMol ]

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SS Bonds (14, 14)

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