3C05 - JenaLib

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Title :   CRYSTAL STRUCTURE OF ACOSTATIN FROM AGKISTRODON CONTORTRIX CONTORTRIX

Authors :   N. Moiseeva, R. Bau, M. Allaire

Date :   18 Jan 08 (Deposition) - 29 Apr 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   Beta-Sheets, Disulfide Bridges, Blood Coagulation, Cell Adhesion, Secreted, Hydrolase, Metal-Binding, Metalloprotease, Protease, Zinc, Zymogen, Blood Clotting/Antitumor Protein Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Moiseeva, R. Bau, S. D. Swenson, F. S. Markland, J. -Y. Choe, Z. -J. Liu, M. Allaire
Crystal Structure Of Acostatin, A Dimeric Disintegrin From Southern Copperhead (Agkistrodon Contortrix Contortrix) At 1. 7 A Resolution
Acta Crystallogr. , Sect. D V. 64 466 2008
PubMed-ID: 18391413 | Reference-DOI: 10.1107/S0907444908002370
(for further references see the PDB file header)

Molecule 1 - DISINTEGRIN ACOSTATIN ALPHA
	Chains	:	A, C
	Fragment	:	UNP RESIDUES 48-109
	Organism Common	:	SOUTHERN COPPERHEAD
	Organism Scientific	:	AGKISTRODON CONTORTRIX CONTORTRIX

Molecule 2 - DISINTEGRIN ACOSTATIN-BETA
	Chains	:	B, D
	Fragment	:	UNP RESIDUES 419-482
	Organism Common	:	SOUTHERN COPPERHEAD
	Organism Scientific	:	AGKISTRODON CONTORTRIX CONTORTRIX

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 3)

No.	Name	Count	Type	Full Name
1	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	SO4	-1	Ligand/Ion	SULFATE ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:25 , LYS A:34 , ARG A:40 , HOH A:79 , HOH A:104 , HOH A:115	BINDING SITE FOR RESIDUE SO4 A 64
2	AC2	SOFTWARE	ALA A:42 , ARG A:43 , GLY A:44 , ASN A:46 , TYR A:49 , LYS A:61 , HOH A:96 , HOH A:111	BINDING SITE FOR RESIDUE SO4 A 65
3	AC3	SOFTWARE	PRO A:47 , ASP A:48 , ARG A:50 , HOH A:89 , HOH A:100	BINDING SITE FOR RESIDUE SO4 A 66

Asymmetric Unit

No.	Residues
1	A:7	-	A:30
2	A:8	-	B:13
3	A:13	-	B:8
4	A:21	-	A:27
5	A:26	-	A:51
6	A:39	-	A:58
7	B:7	-	B:30
8	B:21	-	B:27
9	B:26	-	B:51
10	B:39	-	B:58
11	C:7	-	C:30
12	C:8	-	D:13
13	C:13	-	D:8
14	C:21	-	C:27
15	C:26	-	C:51
16	C:39	-	C:58
17	D:7	-	D:30
18	D:21	-	D:27
19	D:26	-	D:51
20	D:39	-	D:58

(no "Cis Peptide Bond" information available for 3C05)

(no "SAP(SNP)/Variant" information available for 3C05)

Asymmetric Unit (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DISINTEGRIN_2	PS50214	Disintegrin domain profile.	DIDA_AGKCO	51-111	2	A:5-63 C:5-62
2	DISINTEGRIN_1	PS00427	Disintegrins signature.	DIDA_AGKCO	67-86	2	A:21-40 C:21-40
2	DISINTEGRIN_1	PS00427	Disintegrins signature.	VM2AB_AGKCO	439-458	2	B:21-40 D:21-40

Biological Unit 1 (2, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DISINTEGRIN_2	PS50214	Disintegrin domain profile.	DIDA_AGKCO	51-111	1	A:5-63 -
2	DISINTEGRIN_1	PS00427	Disintegrins signature.	DIDA_AGKCO	67-86	1	A:21-40 -
2	DISINTEGRIN_1	PS00427	Disintegrins signature.	VM2AB_AGKCO	439-458	1	B:21-40 -

Biological Unit 2 (2, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DISINTEGRIN_2	PS50214	Disintegrin domain profile.	DIDA_AGKCO	51-111	1	- C:5-62
2	DISINTEGRIN_1	PS00427	Disintegrins signature.	DIDA_AGKCO	67-86	1	- C:21-40
2	DISINTEGRIN_1	PS00427	Disintegrins signature.	VM2AB_AGKCO	439-458	1	- D:21-40

(no "Exon" information available for 3C05)

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:59
 aligned with DIDA_AGKCO | Q805F7 from UniProtKB/Swiss-Prot  Length:111

    Alignment length:59
                                    60        70        80        90       100         
           DIDA_AGKCO    51 NPCCDAATCKLTPGSQCAEGLCCDQCKFIKAGKICRRARGDNPDYRCTGQSGDCPRKHF 109
               SCOP domains d3c05a_ A: automated matches                                SCOP domains
               CATH domains 3c05A00 A:5-63 Echistatin                                   CATH domains
               Pfam domains ----------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....ee...........ee..ee.....eee........ee............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) DISINTEGRIN_2  PDB: A:5-63 UniProt: 51-111                  PROSITE (1)
                PROSITE (2) ----------------DISINTEGRIN_1       ----------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------- Transcript
                 3c05 A   5 NPCCDAATCKLTPGSQCAEGLCCDQCKFIKAGKICRRARGDNPDYRCTGQSGDCPRKHF  63
                                    14        24        34        44        54

Chain B from PDB  Type:PROTEIN  Length:59
 aligned with VM2AB_AGKCO | Q805F6 from UniProtKB/Swiss-Prot  Length:483

    Alignment length:59
                                   431       441       451       461       471         
          VM2AB_AGKCO   422 ANPCCDAATCKLTTGSQCADGLCCDQCKFMKEGTVCRRARGDDLDDYCNGISAGCPRNP 480
               SCOP domains d3c05b_ B: automated matches                                SCOP domains
               CATH domains 3c05B00 B:4-62 Echistatin                                   CATH domains
               Pfam domains ----------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee....ee...........ee..ee.....eee........ee............ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------DISINTEGRIN_1       ---------------------- PROSITE
                 Transcript ----------------------------------------------------------- Transcript
                 3c05 B   4 ANPCCDAATCKLTTGSQCADGLCCDQCKFMKEGTVCRRARGDDLDDYCNGISAGCPRNP  62
                                    13        23        33        43        53

Chain C from PDB  Type:PROTEIN  Length:58
 aligned with DIDA_AGKCO | Q805F7 from UniProtKB/Swiss-Prot  Length:111

    Alignment length:58
                                    60        70        80        90       100        
           DIDA_AGKCO    51 NPCCDAATCKLTPGSQCAEGLCCDQCKFIKAGKICRRARGDNPDYRCTGQSGDCPRKH 108
               SCOP domains d3c05c_ C: automated matches                               SCOP domains
               CATH domains 3c05C00 C:5-62 Echistatin                                  CATH domains
               Pfam domains ---------------------------------------------------------- Pfam domains
         Sec.struct. author ......................ee..ee.....eee........ee............ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) DISINTEGRIN_2  PDB: C:5-62 UniProt: 51-111                 PROSITE (1)
                PROSITE (2) ----------------DISINTEGRIN_1       ---------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------- Transcript
                 3c05 C   5 NPCCDAATCKLTPGSQCAEGLCCDQCKFIKAGKICRRARGDNPDYRCTGQSGDCPRKH  62
                                    14        24        34        44        54

Chain D from PDB  Type:PROTEIN  Length:56
 aligned with VM2AB_AGKCO | Q805F6 from UniProtKB/Swiss-Prot  Length:483

    Alignment length:56
                                   431       441       451       461       471      
          VM2AB_AGKCO   422 ANPCCDAATCKLTTGSQCADGLCCDQCKFMKEGTVCRRARGDDLDDYCNGISAGCP 477
               SCOP domains d3c05d_ D: automated matches                             SCOP domains
               CATH domains 3c05D00 D:4-59 Echistatin                                CATH domains
               Pfam domains -------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee....ee...........ee..ee.....eee........ee......... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------DISINTEGRIN_1       ------------------- PROSITE
                 Transcript -------------------------------------------------------- Transcript
                 3c05 D   4 ANPCCDAATCKLTTGSQCADGLCCDQCKFMKEGTVCRRARGDDLDDYCNGISAGCP  59
                                    13        23        33        43        53

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Small proteins (3458)

Fold: Blood coagulation inhibitor (disintegrin) (24)

Superfamily: Blood coagulation inhibitor (disintegrin) (24)

Family: Blood coagulation inhibitor (disintegrin) (23)

Protein domain: automated matches (4)

Agkistrodon contortrix [TaxId: 8713] (1)

1a	d3c05a_	A:
1b	d3c05b_	B:
1c	d3c05c_	C:
1d	d3c05d_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Few Secondary Structures (1120)

Architecture: Irregular (1120)

Topology: Echistatin (21)

Homologous Superfamily: Echistatin (21)

Southern copperhead (Agkistrodon contortrix contortrix) (1)

1a	3c05A00	A:5-63
1b	3c05C00	C:5-62
1c	3c05B00	B:4-62
1d	3c05D00	D:4-59

(no "Pfam Domain" information available for 3C05)

Asymmetric Unit(hide GO term definitions)

Chain A,C (DIDA_AGKCO | Q805F7)

biological process
	GO:0007155	cell adhesion	The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
	GO:0030195	negative regulation of blood coagulation	Any process that stops, prevents, or reduces the frequency, rate or extent of blood coagulation.
cellular component
	GO:0005575	cellular_component	The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.
	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 (VM2AB_AGKCO | Q805F6)

molecular function
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004222	metalloendopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
	GO:0008237	metallopeptidase activity	Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
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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Description

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Ligands, Modified Residues, Ions (1, 3)

Sites (3, 3)

SS Bonds (20, 20)

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