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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF THE SNAKE VENOM TOXIN AGGRETIN

Authors :   E. Hooley, E. Papagrigoriou, A. Navdaev, A. Pandey, J. M. Clemetson, K. J. Clemetson, J. Emsley

Date :   11 Jan 08 (Deposition) - 26 Aug 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

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

Reference :   E. Hooley, E. Papagrigoriou, A. Navdaev, A. V. Pandey, J. M. Clemetson K. J. Clemetson, J. Emsley
The Crystal Structure Of The Platelet Activator Aggretin Reveals A Novel (Alphabeta)2 Dimeric Structure.
Biochemistry V. 47 7831 2008
PubMed-ID: 18597489 | Reference-DOI: 10.1021/BI800528T

Molecule 1 - AGGRETIN ALPHA CHAIN
	Chains	:	A, C
	Organism Common	:	MALAYAN PIT VIPER
	Organism Scientific	:	AGKISTRODON RHODOSTOMA
	Secretion	:	VENOM

Molecule 2 - AGGRETIN BETA CHAIN
	Chains	:	B, D
	Organism Common	:	MALAYAN PIT VIPER
	Organism Scientific	:	AGKISTRODON RHODOSTOMA
	Secretion	:	VENOM

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

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 10)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	SO4	9	Ligand/Ion	SULFATE ION

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS D:73 , GLY D:74 , CYS D:75 , ASN D:76 , TRP D:77	BINDING SITE FOR RESIDUE SO4 D 124
02	AC2	SOFTWARE	GLY B:74 , CYS B:75 , ASN B:76 , TRP B:77	BINDING SITE FOR RESIDUE SO4 B 124
03	AC3	SOFTWARE	TYR A:12 , GLY A:49 , LYS D:15	BINDING SITE FOR RESIDUE SO4 A 137
04	AC4	SOFTWARE	PHE C:7 , GLY C:8	BINDING SITE FOR RESIDUE SO4 C 137
05	AC5	SOFTWARE	ARG A:75 , GLN A:81 , LYS A:105	BINDING SITE FOR RESIDUE SO4 A 138
06	AC6	SOFTWARE	GLY B:5 , LYS B:15 , TYR C:12 , ASP C:13 , SER C:47 , GLY C:49 , GLU C:50	BINDING SITE FOR RESIDUE SO4 B 125
07	AC7	SOFTWARE	PHE D:17 , ASN D:18 , GLU D:19 , ARG D:58	BINDING SITE FOR RESIDUE SO4 D 125
08	AC8	SOFTWARE	ASN D:70 , HIS D:73	BINDING SITE FOR RESIDUE SO4 D 126
09	AC9	SOFTWARE	ARG C:75 , GLN C:81 , THR C:103 , LYS C:105	BINDING SITE FOR RESIDUE SO4 C 138
10	BC1	SOFTWARE	TRP D:72 , HIS D:73 , TRP D:77	BINDING SITE FOR RESIDUE GOL D 127

Asymmetric/Biological Unit

No.	Residues
1	A:5	-	A:16
2	A:33	-	A:131
3	A:83	-	B:75
4	A:106	-	A:123
5	B:2	-	B:13
6	B:30	-	B:119
7	B:96	-	B:111
8	C:5	-	C:16
9	C:33	-	C:131
10	C:83	-	D:75
11	C:106	-	C:123
12	D:2	-	D:13
13	D:30	-	D:119
14	D:96	-	D:111

(no "Cis Peptide Bond" information available for 3BX4)

(no "SAP(SNP)/Variant" information available for 3BX4)

Asymmetric/Biological Unit (2, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	C_TYPE_LECTIN_2	PS50041	C-type lectin domain profile.	SLYA_CALRH	12-132	2	A:12-132 C:12-132
1	C_TYPE_LECTIN_2	PS50041	C-type lectin domain profile.	SLYB_CALRH	32-143	2	B:9-120 D:9-120
2	C_TYPE_LECTIN_1	PS00615	C-type lectin domain signature.	SLYA_CALRH	106-131	2	A:106-131 C:106-131
2	C_TYPE_LECTIN_1	PS00615	C-type lectin domain signature.	SLYB_CALRH	119-142	2	B:96-119 D:96-119

(no "Exon" information available for 3BX4)

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:132
 aligned with SLYA_CALRH | Q9I841 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:132
                                    13        23        33        43        53        63        73        83        93       103       113       123       133  
           SLYA_CALRH     4 DCDFGWSPYDQHCYQAFNEQKTWDEAEKFCRAQENGAHLASIESNGEADFVSWLISQKDELADEDYVWIGLRAQNKEQQCSSEWSDGSSVSYENLIDLHTKKCGALEKLTGFRKWVNYYCEQMHAFVCKLLP 135
               SCOP domains d3bx4a_ A: automated matches                                                                                                         SCOP domains
               CATH domains 3bx4A00 A:4-135 Mannose-Binding Protein A, subunit A                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......eee..eeeeeeeeeehhhhhhhhhhh.....ee....hhhhhhhhhhhhhhhhhhh...eeeeeeee.............................eeeee.hhh...eeee.....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) --------C_TYPE_LECTIN_2  PDB: A:12-132 UniProt: 12-132                                                                           --- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                PROSITE (3) ------------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1           ---- PROSITE (3)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3bx4 A   4 DCDFGWSPYDQHCYQAFNEQKTWDEAEKFCRAQENGAHLASIESNGEADFVSWLISQKDELADEDYVWIGLRAQNKEQQCSSEWSDGSSVSYENLIDLHTKKCGALEKLTGFRKWVNYYCEQMHAFVCKLLP 135
                                    13        23        33        43        53        63        73        83        93       103       113       123       133

Chain B from PDB  Type:PROTEIN  Length:122
 aligned with SLYB_CALRH | Q9I840 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:122
                                    34        44        54        64        74        84        94       104       114       124       134       144  
           SLYB_CALRH    25 CPSGWSSYEGHCYKPFNEPKNWADAERFCKLQPKHSHLVSFQSAEEADFVVKLTRPRLKANLVWMGLSNIWHGCNWQWSDGARLNYKDWQEQSECLAFRGVHTEWLNMDCSSTCSFVCKFKA 146
               SCOP domains d3bx4b_ B: automated matches                                                                                               SCOP domains
               CATH domains 3bx4B00 B:2-123 Mannose-Binding Protein A, subunit A                                                                       CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee..eeeeeeeeeehhhhhhhhhhhh....ee....hhhhhhhhhhhhh......eee...........eee...............eeeeee.....eeeee....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -------C_TYPE_LECTIN_2  PDB: B:9-120 UniProt: 32-143                                                                   --- PROSITE (2)
                PROSITE (3) -------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) ----------------------------------------------------------------------------------------------C_TYPE_LECTIN_1         ---- PROSITE (4)
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bx4 B   2 CPSGWSSYEGHCYKPFNEPKNWADAERFCKLQPKHSHLVSFQSAEEADFVVKLTRPRLKANLVWMGLSNIWHGCNWQWSDGARLNYKDWQEQSECLAFRGVHTEWLNMDCSSTCSFVCKFKA 123
                                    11        21        31        41        51        61        71        81        91       101       111       121

Chain C from PDB  Type:PROTEIN  Length:134
 aligned with SLYA_CALRH | Q9I841 from UniProtKB/Swiss-Prot  Length:136

    Alignment length:134
                                    12        22        32        42        52        62        72        82        92       102       112       122       132    
           SLYA_CALRH     3 EDCDFGWSPYDQHCYQAFNEQKTWDEAEKFCRAQENGAHLASIESNGEADFVSWLISQKDELADEDYVWIGLRAQNKEQQCSSEWSDGSSVSYENLIDLHTKKCGALEKLTGFRKWVNYYCEQMHAFVCKLLPY 136
               SCOP domains d3bx4c_ C: automated matches                                                                                                           SCOP domains
               CATH domains 3bx4C00 C:3-136 Mannose-Binding Protein A, subunit A                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee..eeeeeeeeeehhhhhhhhhhh.....ee....hhhhhhhhhhhhhhhhhhh...eeeeeeee.............................eeeee.hhh...eeee.....eeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------C_TYPE_LECTIN_2  PDB: C:12-132 UniProt: 12-132                                                                           ---- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (3) -------------------------------------------------------------------------------------------------------C_TYPE_LECTIN_1           ----- PROSITE (3)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bx4 C   3 EDCDFGWSPYDQHCYQAFNEQKTWDEAEKFCRAQENGAHLASIESNGEADFVSWLISQKDELADEDYVWIGLRAQNKEQQCSSEWSDGSSVSYENLIDLHTKKCGALEKLTGFRKWVNYYCEQMHAFVCKLLPY 136
                                    12        22        32        42        52        62        72        82        92       102       112       122       132

Chain D from PDB  Type:PROTEIN  Length:123
 aligned with SLYB_CALRH | Q9I840 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:123
                                    33        43        53        63        73        83        93       103       113       123       133       143   
           SLYB_CALRH    24 DCPSGWSSYEGHCYKPFNEPKNWADAERFCKLQPKHSHLVSFQSAEEADFVVKLTRPRLKANLVWMGLSNIWHGCNWQWSDGARLNYKDWQEQSECLAFRGVHTEWLNMDCSSTCSFVCKFKA 146
               SCOP domains d3bx4d_ D: automated matches                                                                                                SCOP domains
               CATH domains 3bx4D00 D:1-123 Mannose-Binding Protein A, subunit A                                                                        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eee..eeeeeeeeeehhhhhhhhhhh.....ee....hhhhhhhhhhhhhhhhh..eeeeeee.......eee...............eeeeee..eeeeeeee....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) --------C_TYPE_LECTIN_2  PDB: D:9-120 UniProt: 32-143                                                                   --- PROSITE (2)
                PROSITE (3) --------------------------------------------------------------------------------------------------------------------------- PROSITE (3)
                PROSITE (4) -----------------------------------------------------------------------------------------------C_TYPE_LECTIN_1         ---- PROSITE (4)
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 3bx4 D   1 DCPSGWSSYEGHCYKPFNEPKNWADAERFCKLQPKHSHLVSFQSAEEADFVVKLTRPRLKANLVWMGLSNIWHGCNWQWSDGARLNYKDWQEQSECLAFRGVHTEWLNMDCSSTCSFVCKFKA 123
                                    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: Alpha and beta proteins (a+b) (23004)

Fold: C-type lectin-like (322)

Superfamily: C-type lectin-like (322)

Family: C-type lectin domain (182)

Protein domain: automated matches (16)

Agkistrodon rhodostoma [TaxId: 8717] (1)

1a	d3bx4a_	A:
1b	d3bx4b_	B:
1c	d3bx4c_	C:
1d	d3bx4d_	D:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Roll (3276)

Topology: Mannose-Binding Protein A; Chain A (180)

Homologous Superfamily: Mannose-Binding Protein A, subunit A (180)

Malayan pit viper (Agkistrodon rhodostoma) (1)

1a	3bx4C00	C:3-136
1b	3bx4A00	A:4-135
1c	3bx4D00	D:1-123
1d	3bx4B00	B:2-123

(no "Pfam Domain" information available for 3BX4)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,C (SLYA_CALRH | Q9I841)

molecular function
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0060300	regulation of cytokine activity	Any process that modulates the rate, frequency or extent of the activity of a molecule that controls the survival, growth, differentiation and effector function of tissues and cells.
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.

Chain B,D (SLYB_CALRH | Q9I840)

molecular function
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
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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	3bx4
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(no "Related Entries Specified in the PDB File" available for 3BX4)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 10)

Sites (10, 10)

SS Bonds (14, 14)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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