3QNL - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF PRTX-I COMPLEXED TO ROSMARINIC ACID

Authors :   J. I. Dos Santos, M. R. M. Fontes

Date :   08 Feb 11 (Deposition) - 29 Feb 12 (Release) - 09 Apr 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.77

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

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

Reference :   J. I. Dos Santos, F. F. Cardoso, A. M. Soares, M. Dal Pai Silva, M. Gallacci, M. R. Fontes
Structural And Functional Studies Of A Bothropic Myotoxin Complexed To Rosmarinic Acid: New Insights Into Lys49-Pla(2 Inhibition.
Plos One V. 6 28521 2011
PubMed-ID: 22205953 | Reference-DOI: 10.1371/JOURNAL.PONE.0028521

Molecule 1 - PHOSPHOLIPASE A2 HOMOLOG 1
	Chains	:	A, B
	Organism Common	:	PIRAJA'S LANCE HEAD
	Organism Scientific	:	BOTHROPS PIRAJAI
	Organism Taxid	:	113192
	Synonym	:	MYOTOXIN SIV-SP5, PIRATOXIN-I, PRTX-I

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 10)

No.	Name	Count	Type	Full Name
1	IPA	8	Ligand/Ion	ISOPROPYL ALCOHOL
2	P33	1	Ligand/Ion	3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL
3	ROA	1	Ligand/Ion	(2R)-3-(3,4-DIHYDROXYPHENYL)-2-{[(2E)-3-(3,4-DIHYDROXYPHENYL)PROP-2-ENOYL]OXY}PROPANOIC ACID

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	TYR A:22 , CYS A:29 , GLY A:30 , IPA A:202 , HOH A:381	BINDING SITE FOR RESIDUE IPA A 201
02	AC2	SOFTWARE	IPA A:201 , HOH A:410	BINDING SITE FOR RESIDUE IPA A 202
03	AC3	SOFTWARE	LYS A:115 , ARG A:118 , HOH A:411	BINDING SITE FOR RESIDUE IPA A 203
04	AC4	SOFTWARE	ASN A:87 , ASN A:88 , GLU A:108 , HOH A:394 , IPA B:203	BINDING SITE FOR RESIDUE IPA A 204
05	AC5	SOFTWARE	PHE A:3 , LYS A:7 , LEU A:10 , GLN A:11 , GLY A:15 , HOH A:395 , HOH A:399 , HOH A:426 , HOH A:427 , LYS B:7 , LEU B:10 , GLN B:11 , TRP B:77 , P33 B:205	BINDING SITE FOR RESIDUE ROA A 205
06	AC6	SOFTWARE	CYS B:29 , GLY B:30 , P33 B:205 , HOH B:386	BINDING SITE FOR RESIDUE IPA B 201
07	AC7	SOFTWARE	ARG B:72	BINDING SITE FOR RESIDUE IPA B 202
08	AC8	SOFTWARE	IPA A:204 , HOH A:379 , LYS B:53 , LYS B:57 , HOH B:361 , HOH B:381	BINDING SITE FOR RESIDUE IPA B 203
09	AC9	SOFTWARE	LYS B:36 , PRO B:37 , LYS B:38	BINDING SITE FOR RESIDUE IPA B 204
10	BC1	SOFTWARE	LEU A:10 , PRO A:123 , ROA A:205 , LEU B:2 , LEU B:121 , IPA B:201	BINDING SITE FOR RESIDUE P33 B 205

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:29	-	B:45
9	B:44	-	B:105
10	B:50	-	B:133
11	B:51	-	B:98
12	B:61	-	B:91
13	B:84	-	B:96

(no "Cis Peptide Bond" information available for 3QNL)

(no "SAP(SNP)/Variant" information available for 3QNL)

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.	PA2H1_BOTPI	43-50	2	A:44-51 B:44-51
2	PA2_ASP	PS00119	Phospholipase A2 aspartic acid active site.	PA2H1_BOTPI	85-95	2	A:95-105 B:95-105

(no "Exon" information available for 3QNL)

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 PA2H1_BOTPI | P58399 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:121
                                    10        20        30        40        50        60        70        80        90       100       110       120 
          PA2H1_BOTPI     1 SLFELGKMILQETGKNPAKSYGAYGCNCGVLGRGKPKDATDRCCYVHKCCYKKLTGCNPKKDRYSYSWKDKTIVCGENNPCLKELCECDKAVAICLRENLGTYNKLYRYHLKPFCKKADDC 121
               SCOP domains d3qnla_ A: automated matches                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhhh...............hhhhhhhhhhhhhhhhh...........eeee..eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS ----------------------------------PA2_ASP    -------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qnl A   1 SLFELGKMILQETGKNPAKSYGAYGCNCGVLGRGKPKDATDRCCYVHKCCYKKLTGCNPKKDRYSYSWKDKTIVCGENNPCLKELCECDKAVAICLRENLGTYNKLYRYHLKPFCKKADDC 133
                                    10  ||    21        31        41        51 ||   ||69        79        90       100       110       120  || ||132 
                                       13|                                    53|  61|                   88|                              123| ||    
                                        15                                     57   67                    90                               125 ||    
                                                                                                                                             127|    
                                                                                                                                              129

Chain B from PDB  Type:PROTEIN  Length:121
 aligned with PA2H1_BOTPI | P58399 from UniProtKB/Swiss-Prot  Length:121

    Alignment length:121
                                    10        20        30        40        50        60        70        80        90       100       110       120 
          PA2H1_BOTPI     1 SLFELGKMILQETGKNPAKSYGAYGCNCGVLGRGKPKDATDRCCYVHKCCYKKLTGCNPKKDRYSYSWKDKTIVCGENNPCLKELCECDKAVAICLRENLGTYNKLYRYHLKPFCKKADDC 121
               SCOP domains d3qnlb_ B: automated matches                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.hhhhhhhee...ee........hhhhhhhhhhhhhhhh............eeee..eeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------PA2_HIS ----------------------------------PA2_ASP    -------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qnl B   1 SLFELGKMILQETGKNPAKSYGAYGCNCGVLGRGKPKDATDRCCYVHKCCYKKLTGCNPKKDRYSYSWKDKTIVCGENNPCLKELCECDKAVAICLRENLGTYNKLYRYHLKPFCKKADDC 133
                                    10  ||    21        31        41        51 ||   ||69        79        90       100       110       120  || ||132 
                                       13|                                    53|  61|                   88|                              123| ||    
                                        15                                     57   67                    90                               125 ||    
                                                                                                                                             127|    
                                                                                                                                              129

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)

Bothrops pirajai [TaxId: 113192] (2)

1a	d3qnla_	A:
1b	d3qnlb_	B:

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (PA2H1_BOTPI | P58399)

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: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
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3qnl)

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	3qnl
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UniProtKB/Swiss-Prot
	PA2H1_BOTPI \| P58399	:	2ok9 2q2j 4yu7 4yz7

1pa0	BNSP-7 IN APO FORM
1qll	PRTX-II COMPLEXED TO FATTY ACID
1xxs	MJTX-II COMPLEXED TO STEARIC ACID
1y4l	BASPTX-II COMPLEXED TO SURAMIN
2ok9	THE SAME PROTEIN COMPLEXED TO BPB
2q2j	THE SAME PROTEIN IN APO FORM
3cxi	BTHTX-I COMPLEXED TO ALPHA-TOCOPHEROL
3cyl	PRTX-I COMPLEXED TO ALPHA-TOCOPHEROL
3i3h	BTHTX-I IN APO FORM

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 10)

Sites (10, 10)

SS Bonds (13, 13)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (0, 0)

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SCOP Domains (1, 2)

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Pfam Domains (0, 0)

Gene Ontology (4, 4)

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