2USN - JenaLib

Title :   CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN FIBROBLAST STROMELYSIN-1 INHIBITED WITH THIADIAZOLE INHIBITOR PNU-141803

Authors :   B. C. Finzel, G. L. Bryant Junior, E. T. Baldwin

Date :   09 Jun 98 (Deposition) - 23 Dec 98 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

Chains :   Asym./Biol. Unit : A

Keywords :   Hydrolase, Metalloprotease, Fibroblast, Collagen Degradation (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. C. Finzel, E. T. Baldwin, G. L. Bryant Jr. , G. F. Hess, J. W. Wilks, C. M. Trepod, J. E. Mott, V. P. Marshall, G. L. Petzold, R. A. Poorman, T. J. O'Sullivan, H. J. Schostarez, M. A. Mitchell
Structural Characterizations Of Nonpeptidic Thiadiazole Inhibitors Of Matrix Metalloproteinases Reveal The Basis For Stromelysin Selectivity.
Protein Sci. V. 7 2118 1998
PubMed-ID: 9792098
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 7)

Sites (10, 10)

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:201 , HIS A:205 , HIS A:211 , IN8 A:300	BINDING SITE FOR RESIDUE ZN A 257
02	AC2	SOFTWARE	HIS A:151 , ASP A:153 , HIS A:166 , HIS A:179	BINDING SITE FOR RESIDUE ZN A 258
03	AC3	SOFTWARE	ASP A:158 , GLY A:159 , GLY A:161 , VAL A:163 , ASP A:181 , GLU A:184	BINDING SITE FOR RESIDUE CA A 259
04	AC4	SOFTWARE	ASP A:141 , GLY A:173 , ASN A:175 , ASP A:177 , HOH A:307 , HOH A:316	BINDING SITE FOR RESIDUE CA A 260
05	AC5	SOFTWARE	ASP A:107 , ASP A:182 , GLU A:184 , HOH A:321 , HOH A:331	BINDING SITE FOR RESIDUE CA A 261
06	AC6	SOFTWARE	HIS A:96 , HOH A:263	BINDING SITE FOR RESIDUE ZN A 262
07	AC7	SOFTWARE	PRO A:90 , TYR A:155 , HIS A:166 , ALA A:167 , TYR A:168 , ALA A:169 , ASN A:175 , HIS A:201 , GLU A:202 , HIS A:205 , PHE A:210 , HIS A:211 , ZN A:257 , HOH A:380	BINDING SITE FOR RESIDUE IN8 A 300
08	INH	UNKNOWN	PHE A:86 , TYR A:155 , HIS A:166 , ALA A:167 , TYR A:168 , ALA A:169 , HIS A:205 , PHE A:210	SITE INH IS THE BINDING SITE FOR THE AMIDE- THIADIAZOLE INHIBITOR PNU-141803; IN8 300.
09	ZN1	UNKNOWN	HIS A:201 , HIS A:205 , HIS A:211 , IN8 A:300	ZN1 ARE THE LIGANDS OF THE CATALYTIC (ZN 257) ZINC ION.
10	ZN2	UNKNOWN	HIS A:151 , ASP A:153 , HIS A:166 , HIS A:179	ZN2 ARE THE LIGANDS OF THE STRUCTURAL (ZN 258) ZINC ION.

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (5, 5)

Sequences/Alignments

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:165
 aligned with MMP3_HUMAN | P08254 from UniProtKB/Swiss-Prot  Length:477

    Alignment length:165
                                   109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259     
           MMP3_HUMAN   100 FRTFPGIPKWRKTHLTYRIVNYTPDLPKDAVDSAVEKALKVWEEVTPLTFSRLYEGEADIMISFAVREHGDFYPFDGPGNVLAHAYAPGPGINGDAHFDDDEQWTKDTTGTNLFLVAAHEIGHSLGLFHSANTEALMYPLYHSLTDLTRFRLSQDDINGIQSLYG 264
               SCOP domains d2usna_ A: Stromelysin-1 (MMP-3)                                                                                                                                      SCOP domains
               CATH domains 2usnA00 A:83-247 Collagenase (Catalytic Domain)                                                                                                                       CATH domains
               Pfam domains --------Peptidase_M10-2usnA01 A:91-247                                                                                                                                Pfam domains
         Sec.struct. author .............eeeeee........hhhhhhhhhhhhhhhh.....eeee.......eeeeee.................eee..........eeee.............hhhhhhhhhhhhh...............hhhh..hhh....hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------ZINC_PROTE---------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2          -------------------------------------------------Exon 1.4b  PDB: A:150-192 UniProt: 167-209 ------------------------------------------------------1 Transcript 1 (1)
           Transcript 1 (2) -----------------Exon 1.3  PDB: A:100-150 UniProt: 117-167          -----------------------------------------Exon 1.5  PDB: A:192-247 UniProt: 209-264                Transcript 1 (2)
                 2usn A  83 FRTFPGIPKWRKTHLTYRIVNYTPDLPKDAVDSAVEKALKVWEEVTPLTFSRLYEGEADIMISFAVREHGDFYPFDGPGNVLAHAYAPGPGINGDAHFDDDEQWTKDTTGTNLFLVAAHEIGHSLGLFHSANTEALMYPLYHSLTDLTRFRLSQDDINGIQSLYG 247
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242

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, 1)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (MMP3_HUMAN | P08254)

molecular function
	GO:0005509	calcium ion binding	Interacting selectively and non-covalently with calcium ions (Ca2+).
	GO:0004175	endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain.
	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:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0004252	serine-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0071732	cellular response to nitric oxide	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nitric oxide stimulus.
	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:0022617	extracellular matrix disassembly	A process that results in the breakdown of the extracellular matrix.
	GO:0010727	negative regulation of hydrogen peroxide metabolic process	Any process that decreases the frequency, rate or extent of the chemical reactions and pathways involving hydrogen peroxide.
	GO:1903209	positive regulation of oxidative stress-induced cell death	Any process that activates or increases the frequency, rate or extent of oxidative stress-induced cell death.
	GO:0032461	positive regulation of protein oligomerization	Any process that activates or increases the frequency, rate or extent of protein oligomerization.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
	GO:0031012	extracellular matrix	A structure lying external to one or more cells, which provides structural support for cells or tissues.
	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:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
	GO:0005578	proteinaceous extracellular matrix	A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. An example of this component is found in Mus musculus.

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