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Description

Title :   STRUCTURE BASIS OF VENOM CITRATE-DEPENDENT HEPARIN SULFATE-MEDIATED CELL SURFACE RETENTION OF COBRA CARDIOTOXIN A3

Authors :   S. -C. Lee, H. -H. Guan, C. -H. Wang, W. -N. Huang, C. -J. Chen, W. -G. Wu

Date :   21 Oct 04 (Deposition) - 14 Dec 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

Keywords :   Ctx-3, Heparin, Citrate, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. -C. Lee, H. -H. Guan, C. -H. Wang, W. -N. Huang, S. -C. Tjong, C. -J. Chen, W. -G. Wu
Structural Basis Of Citrate-Dependent And Heparan Sulfate-Mediated Cell Surface Retention Of Cobra Cardiotoxi A3
J. Biol. Chem. V. 280 9567 2005
PubMed-ID: 15590643 | Reference-DOI: 10.1074/JBC.M412398200

Compounds

Molecule 1 - CYTOTOXIN 3
	Chains	:	A, B
	Organism Common	:	CHINESE COBRA
	Organism Scientific	:	NAJA ATRA
	Organism Taxid	:	8656
	Synonym	:	CARDIOTOXIN 3, CTX-3, CARDIOTOXIN ANALOG III, CTX III

Structural Features

Chains, Units

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

Summary Information (see also Sequences/Alignments below)

Ligands, Modified Residues, Ions (3, 7)

Asymmetric Unit (3, 7)

No.	Name	Count	Type	Full Name
1	CIT	1	Ligand/Ion	CITRIC ACID
2	IDS	3	Ligand/Ion	2-O-SULFO-ALPHA-L-IDOPYRANURONIC ACID
3	SGN	3	Ligand/Ion	N,O6-DISULFO-GLUCOSAMINE

Biological Unit 1 (3, 7)

No.	Name	Count	Type	Full Name
1	CIT	1	Ligand/Ion	CITRIC ACID
2	IDS	3	Ligand/Ion	2-O-SULFO-ALPHA-L-IDOPYRANURONIC ACID
3	SGN	3	Ligand/Ion	N,O6-DISULFO-GLUCOSAMINE

Sites (7, 7)

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:6 , LYS A:12 , TYR A:22 , LYS A:35 , ARG A:36 , GLY A:37 , SGN A:62 , LYS B:5	BINDING SITE FOR RESIDUE IDS A 61
2	AC2	SOFTWARE	LYS A:18 , IDS A:61 , IDS A:63 , SER B:45 , SER B:46	BINDING SITE FOR RESIDUE SGN A 62
3	AC3	SOFTWARE	SGN A:62 , SGN A:64 , LYS B:44	BINDING SITE FOR RESIDUE IDS A 63
4	AC4	SOFTWARE	IDS A:63 , IDS A:65	BINDING SITE FOR RESIDUE SGN A 64
5	AC5	SOFTWARE	SGN A:64 , SGN A:66	BINDING SITE FOR RESIDUE IDS A 65
6	AC6	SOFTWARE	IDS A:65 , HOH A:104	BINDING SITE FOR RESIDUE SGN A 66
7	AC7	SOFTWARE	LYS A:23 , LYS A:31 , CYS A:59 , LYS B:23 , PRO B:30 , LYS B:31	BINDING SITE FOR RESIDUE CIT A 101

SS Bonds (9, 9)

Asymmetric Unit

No.	Residues
1	A:3	-	A:21
2	A:14	-	A:38
3	A:42	-	A:53
4	A:54	-	A:59
5	B:3	-	B:21
6	B:3	-	B:14
7	B:14	-	B:38
8	B:42	-	B:53
9	B:54	-	B:59

Cis Peptide Bonds (0, 0)

(no "Cis Peptide Bond" information available for 1XT3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

(no "SAP(SNP)/Variant" information available for 1XT3)

PROSITE Motifs (1, 2)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SNAKE_TOXIN	PS00272	Snake toxins signature.	3SA3_NAJAT	58-78	2	A:37-57 B:37-57

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SNAKE_TOXIN	PS00272	Snake toxins signature.	3SA3_NAJAT	58-78	2	A:37-57 B:37-57

Exons (0, 0)

(no "Exon" information available for 1XT3)

Sequences/Alignments

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:60
 aligned with 3SA3_NAJAT | P60301 from UniProtKB/Swiss-Prot  Length:81

    Alignment length:60
                                    31        41        51        61        71        81
            3SA3_NAJAT   22 LKCNKLVPLFYKTCPAGKNLCYKMFMVATPKVPVKRGCIDVCPKSSLLVKYVCCNTDRCN 81
               SCOP domains d1xt3a_ A: Cardiotoxin III                                   SCOP domains
               CATH domains 1xt3A00 A:1-60 CD59                                          CATH domains
               Pfam domains ------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee......eee.......eeeeee........eeee..........eeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------SNAKE_TOXIN          --- PROSITE
                 Transcript ------------------------------------------------------------ Transcript
                  1xt3 A  1 LKCNKLVPLFYKTCPAGKNLCYKMFMVATPKVPVKRGCIDVCPKSSLLVKYVCCNTDRCN 60
                                    10        20        30        40        50        60

Chain B from PDB  Type:PROTEIN  Length:60
 aligned with 3SA3_NAJAT | P60301 from UniProtKB/Swiss-Prot  Length:81

    Alignment length:60
                                    31        41        51        61        71        81
            3SA3_NAJAT   22 LKCNKLVPLFYKTCPAGKNLCYKMFMVATPKVPVKRGCIDVCPKSSLLVKYVCCNTDRCN 81
               SCOP domains d1xt3b_ B: Cardiotoxin III                                   SCOP domains
               CATH domains 1xt3B00 B:1-60 CD59                                          CATH domains
               Pfam domains ------------------------------------------------------------ Pfam domains
         Sec.struct. author ....................eeeeee........eeee..........eeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------SNAKE_TOXIN          --- PROSITE
                 Transcript ------------------------------------------------------------ Transcript
                  1xt3 B  1 LKCNKLVPLFYKTCPAGKNLCYKMFMVATPKVPVKRGCIDVCPKSSLLVKYVCCNTDRCN 60
                                    10        20        30        40        50        60

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 '\|'

Classification and Annotation

SCOP Domains (1, 2)

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Small proteins (3458)

Fold: Snake toxin-like (152)

Superfamily: Snake toxin-like (152)

Family: Snake venom toxins (107)

Protein domain: Cardiotoxin III (6)

Taiwan cobra (Naja naja atra) [TaxId: 8656] (6)

1a	d1xt3a_	A:
1b	d1xt3b_	B:

CATH Domains (1, 2)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Ribbon (789)

Topology: CD59 (129)

Homologous Superfamily: CD59 (129)

Chinese cobra (Naja atra) (20)

1a	1xt3A00	A:1-60
1b	1xt3B00	B:1-60

Pfam Domains (0, 0)

(no "Pfam Domain" information available for 1XT3)

Gene Ontology (7, 7)

Asymmetric Unit(hide GO term definitions)

Chain A,B (3SA3_NAJAT | P60301)

biological process
	GO:0019835	cytolysis	The rupture of cell membranes and the loss of cytoplasm.
	GO:0044179	hemolysis in other organism	The cytolytic destruction of red blood cells, with the release of intracellular hemoglobin, in one organism by another.
	GO:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
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.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0044218	other organism cell membrane	The cell membrane of a secondary organism with which the first organism is interacting.
	GO:0044279	other organism membrane	A membrane of a secondary organism with which the first organism is interacting.

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	Cis Peptide Bonds
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	1xt3
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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
	3SA3_NAJAT \| P60301	:	1h0j 1i02 2bhi 2crs 2crt

Related Entries Specified in the PDB File

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