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Title :   STRUCTURAL INTERACTION OF NATURAL AND SYNTHETIC INHIBITORS WITH THE VENOM METALLOPROTEINASE, ATROLYSIN C (HT-D)

Authors :   D. Zhang, I. Botos, F. -X. Gomis-Rueth, R. Doll, C. Blood, F. G. Njoroge, J. W. Fox, W. Bode, E. F. Meyer

Date :   20 Jan 94 (Deposition) - 15 Sep 95 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

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

Reference :   D. Zhang, I. Botos, F. X. Gomis-Ruth, R. Doll, C. Blood, F. G. Njoroge, J. W. Fox, W. Bode, E. F. Meyer
Structural Interaction Of Natural And Synthetic Inhibitors With The Venom Metalloproteinase, Atrolysin C (Form D).
Proc. Natl. Acad. Sci. Usa V. 91 8447 1994
PubMed-ID: 8078901 | Reference-DOI: 10.1073/PNAS.91.18.8447
(for further references see the PDB file header)

Molecule 1 - ATROLYSIN C
	Chains	:	A, B
	EC Number	:	3.4.24.42
	Organism Common	:	WESTERN DIAMONDBACK RATTLESNAKE
	Organism Scientific	:	CROTALUS ATROX
	Organism Taxid	:	8730
	Other Details	:	ISOLATED FROM VENOM
	Synonym	:	HEMORRHAGIC TOXIN C, FORM D

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	CA	2	Ligand/Ion	CALCIUM ION
2	ZN	2	Ligand/Ion	ZINC ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:142 , HIS A:146 , HIS A:152 , HOH A:479	BINDING SITE FOR RESIDUE ZN A 401
2	AC2	SOFTWARE	GLU A:9 , ASP A:93 , CYS A:197 , ASN A:200 , HOH A:416 , HOH A:430	BINDING SITE FOR RESIDUE CA A 403
3	AC3	SOFTWARE	HIS B:142 , HIS B:146 , HIS B:152 , HOH B:302	BINDING SITE FOR RESIDUE ZN B 402
4	AC4	SOFTWARE	GLU B:9 , ASP B:93 , CYS B:197 , ASN B:200 , HOH B:349 , HOH B:357	BINDING SITE FOR RESIDUE CA B 404
5	CAA	AUTHOR	GLU A:9 , ASP A:93 , ASN A:200	CALCIUM ION BINDING SITE IN CHAIN A
6	CAB	AUTHOR	GLU B:9 , ASP B:93 , ASN B:200	CALCIUM ION BINDING SITE IN CHAIN B
7	ZNA	AUTHOR	HIS A:142 , HIS A:146 , HIS A:152	ZINC BINDING SITE IN CHAIN A. THEY ARE IDENTIFIED BY CONSERVED RESIDUES HEXXHXXGXXH IN BOTH VENOM AND MAMMALIAN COLLAGENASES
8	ZNB	AUTHOR	HIS B:142 , HIS B:146 , HIS B:152	ZINC BINDING SITE IN CHAIN B. THEY ARE IDENTIFIED BY CONSERVED RESIDUES HEXXHXXGXXH IN BOTH VENOM AND MAMMALIAN COLLAGENASES

Asymmetric/Biological Unit

No.	Residues
1	A:117	-	A:197
2	A:157	-	A:164
3	B:117	-	B:197
4	B:157	-	B:164

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

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

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADAM_MEPRO	PS50215	ADAM type metalloprotease domain profile.	VM1AD_CROAT	197-393	2	A:6-202 B:6-202
2	ZINC_PROTEASE	PS00142	Neutral zinc metallopeptidases, zinc-binding region signature.	VM1AD_CROAT	330-339	2	A:139-148 B:139-148

(no "Exon" information available for 1HTD)

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
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Chain A from PDB  Type:PROTEIN  Length:200
 aligned with VM1AD_CROAT | P15167 from UniProtKB/Swiss-Prot  Length:414

    Alignment length:200
                                   203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393
          VM1AD_CROAT   194 LPQRYIELVVVADHRVFMKYNSDLNTIRTRVHEIVNFINGFYRSLNIHVSLTDLEIWSNEDQINIQSASSDTLNAFAEWRETDLLNRKSHDNAQLLTAIELDEETLGLAPLGTMCDPKLSIGIVQDHSPINLLMGVTMAHELGHNLGMEHDGKDCLRGASLCIMRPGLTKGRSYEFSDDSMHYYERFLKQYKPQCILNKP 393
               SCOP domains d1htda_ A: Snake venom metalloprotease                                                                                                                                                                   SCOP domains
               CATH domains 1htdA00 A:3-202 Collagenase (Catalytic Domain)                                                                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee.hhhhhhh...hhhhhhhhhhhhhhhhhhhh...eeeeeeeeeee...........hhhhhhhhhhhhhhhhhhhh..eeeeeeee.......eeeee.........eeeeeee....hhhhhhhhhhhhhhhh...eeeeee........eeeeeee.......hhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---ADAM_MEPRO  PDB: A:6-202 UniProt: 197-393                                                                                                                                                             PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------ZINC_PROTE------------------------------------------------------ PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1htd A   3 LPQRYIELVVVADHRVFMKYNSDLNTIRTRVHEIVNFINGFYRSLNIHVSLTDLEIWSNEDQINIQSASSDTLNAFAEWRETDLLNRKSHDNAQLLTAIELDEETLGLAPLGTMCDPKLSIGIVQDHSPINLLMGVTMAHELGHNLGMEHDGKDCLRGASLCIMRPGLTKGRSYEFSDDSMHYYERFLKQYKPQCILNKP 202
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202

Chain B from PDB  Type:PROTEIN  Length:200
 aligned with VM1AD_CROAT | P15167 from UniProtKB/Swiss-Prot  Length:414

    Alignment length:200
                                   203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393
          VM1AD_CROAT   194 LPQRYIELVVVADHRVFMKYNSDLNTIRTRVHEIVNFINGFYRSLNIHVSLTDLEIWSNEDQINIQSASSDTLNAFAEWRETDLLNRKSHDNAQLLTAIELDEETLGLAPLGTMCDPKLSIGIVQDHSPINLLMGVTMAHELGHNLGMEHDGKDCLRGASLCIMRPGLTKGRSYEFSDDSMHYYERFLKQYKPQCILNKP 393
               SCOP domains d1htdb_ B: Snake venom metalloprotease                                                                                                                                                                   SCOP domains
               CATH domains 1htdB00 B:3-202 Collagenase (Catalytic Domain)                                                                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeeee.hhhhhhh...hhhhhhhhhhhhhhhhhhhh...eeeeeeeeeee...........hhhhhhhhhhhhhhhhhhhh..eeeeeeee.......eeeee.........eeeeeee....hhhhhhhhhhhhhhhh...eeeeee........eeeeeee.......hhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---ADAM_MEPRO  PDB: B:6-202 UniProt: 197-393                                                                                                                                                             PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------------------------------------------------------------------ZINC_PROTE------------------------------------------------------ PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1htd B   3 LPQRYIELVVVADHRVFMKYNSDLNTIRTRVHEIVNFINGFYRSLNIHVSLTDLEIWSNEDQINIQSASSDTLNAFAEWRETDLLNRKSHDNAQLLTAIELDEETLGLAPLGTMCDPKLSIGIVQDHSPINLLMGVTMAHELGHNLGMEHDGKDCLRGASLCIMRPGLTKGRSYEFSDDSMHYYERFLKQYKPQCILNKP 202
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202

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: Zincin-like (701)

Superfamily: Metalloproteases (zincins), catalytic domain (647)

Family: Reprolysin-like (24)

Protein domain: Snake venom metalloprotease (20)

Western diamonback rattlesnake (Crotalus atrox), atrolysin C [TaxId: 8730] (3)

1a	d1htda_	A:
1b	d1htdb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Collagenase (Catalytic Domain) (236)

Homologous Superfamily: Collagenase (Catalytic Domain) (234)

Western diamondback rattlesnake (Crotalus atrox) (3)

1a	1htdA00	A:3-202
1b	1htdB00	B:3-202

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (VM1AD_CROAT | P15167)

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:0030574	collagen catabolic process	The proteolytic chemical reactions and pathways resulting in the breakdown of collagen in the extracellular matrix, usually carried out by proteases secreted by nearby cells.
	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.

Asymmetric/Biological Unit
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Description

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Ligands, Modified Residues, Ions (2, 4)

Sites (8, 8)

SS Bonds (4, 4)

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