1ATL - JenaLib

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Biological Unit 3 (Jmol Viewer)

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

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

Date :   26 May 95 (Deposition) - 15 Oct 95 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym. Unit : A,B
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: A  (1x)
Biol. Unit 3: B  (1x)

Keywords :   Metalloendopeptidase, Hydrolase-Hydrolase Inhibitor Complex (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 Unit	:	A	B
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:	A
Biological Unit 3 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 6)

No.	Name	Count	Type	Full Name
1	0QI	2	Ligand/Ion	O-METHYL-N-[(2S)-4-METHYL-2-(SULFANYLMETHYL)PENTANOYL]-L-TYROSINE
2	CA	2	Ligand/Ion	CALCIUM ION
3	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	0QI	2	Ligand/Ion	O-METHYL-N-[(2S)-4-METHYL-2-(SULFANYLMETHYL)PENTANOYL]-L-TYROSINE
2	CA	-1	Ligand/Ion	CALCIUM ION
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	0QI	1	Ligand/Ion	O-METHYL-N-[(2S)-4-METHYL-2-(SULFANYLMETHYL)PENTANOYL]-L-TYROSINE
2	CA	-1	Ligand/Ion	CALCIUM ION
3	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	0QI	1	Ligand/Ion	O-METHYL-N-[(2S)-4-METHYL-2-(SULFANYLMETHYL)PENTANOYL]-L-TYROSINE
2	CA	-1	Ligand/Ion	CALCIUM ION
3	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:142 , HIS A:146 , HIS A:152 , 0QI A:301	BINDING SITE FOR RESIDUE ZN A 401
2	AC2	SOFTWARE	GLU A:9 , ASP A:93 , CYS A:197 , ASN A:200 , HOH A:814	BINDING SITE FOR RESIDUE CA A 403
3	AC3	SOFTWARE	HIS B:142 , HIS B:146 , HIS B:152 , 0QI B:311	BINDING SITE FOR RESIDUE ZN B 402
4	AC4	SOFTWARE	GLU B:9 , ASP B:93 , CYS B:197 , ASN B:200 , HOH B:834 , HOH B:921	BINDING SITE FOR RESIDUE CA B 404
5	AC5	SOFTWARE	GLU A:106 , THR A:107 , LEU A:108 , GLY A:109 , HIS A:142 , GLU A:143 , HIS A:146 , HIS A:152 , ILE A:165 , ARG A:167 , PRO A:168 , GLY A:169 , LEU A:170 , ZN A:401	BINDING SITE FOR RESIDUE 0QI A 301
6	AC6	SOFTWARE	GLU B:106 , THR B:107 , LEU B:108 , GLY B:109 , HIS B:142 , GLU B:143 , HIS B:146 , HIS B:152 , ILE B:165 , ARG B:167 , PRO B:168 , GLY B:169 , LEU B:170 , ZN B:402 , HOH B:819 , HOH B:920	BINDING SITE FOR RESIDUE 0QI B 311

Asymmetric 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 1ATL)

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

Asymmetric 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

Biological Unit 1 (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

Biological Unit 2 (2, 2)

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

Biological Unit 3 (2, 2)

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

(no "Exon" information available for 1ATL)

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: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 d1atla_ A: Snake venom metalloprotease                                                                                                                                                                   SCOP domains
               CATH domains 1atlA00 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
                 1atl 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 d1atlb_ B: Snake venom metalloprotease                                                                                                                                                                   SCOP domains
               CATH domains 1atlB00 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
                 1atl 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 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	d1atla_	A:
1b	d1atlb_	B:

Asymmetric 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	1atlA00	A:3-202
1b	1atlB00	B:3-202

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

Asymmetric 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 Unit
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	Cis Peptide Bonds
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	1atl
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	VM1AD_CROAT \| P15167
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	3.4.24.42
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	VM1AD_CROAT \| P15167	:	1dth 1htd

(no "Related Entries Specified in the PDB File" available for 1ATL)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (4, 4)

Cis Peptide Bonds (0, 0)

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