1HFS - JenaLib

Title :   CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF HUMAN FIBROBLAST STROMELYSIN-1 INHIBITED WITH THE N-CARBOXY-ALKYL INHIBITOR L-764,004

Authors :   J. W. Becker

Date :   13 Feb 97 (Deposition) - 18 Feb 98 (Release) - 22 Feb 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   Hydrolase, Metalloprotease, Matrix Metalloprotease-3, Proteoglycanase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. K. Esser, R. L. Bugianesi, C. G. Caldwell, K. T. Chapman, P. L. Durette, N. N. Girotra, I. E. Kopka, T. J. Lanza, D. A. Levorse, M. Maccoss, K. A. Owens, M. M. Ponpipom, J. P. Simeone, R. K. Harrison, L. Niedzwiecki, J. W. Becker, A. I. Marcy, M. G. Axel, A. J. Christen, J. Mcdonnell, V. L. Moore, J. M. Olszewski, C. Saphos, D. M. Visco, F. Shen, A. Colletti, P. A. Krieter, W. K. Hagmann
Inhibition Of Stromelysin-1 (Mmp-3) By P1'-Biphenylylethyl Carboxyalkyl Dipeptides.
J. Med. Chem. V. 40 1026 1997
PubMed-ID: 9083493 | Reference-DOI: 10.1021/JM960465T
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (12, 12)

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:201 , HIS A:205 , HIS A:211 , L04 A:256	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:306 , HOH A:312	BINDING SITE FOR RESIDUE CA A 260
05	AC5	SOFTWARE	ASP A:107 , ASP A:182 , GLU A:184 , HOH A:313 , HOH A:332	BINDING SITE FOR RESIDUE CA A 261
06	AC6	SOFTWARE	TYR A:155 , ASN A:162 , VAL A:163 , LEU A:164 , ALA A:165 , HIS A:166 , ALA A:167 , TYR A:168 , HIS A:201 , GLU A:202 , HIS A:205 , HIS A:211 , LEU A:218 , TYR A:220 , PRO A:221 , LEU A:222 , TYR A:223 , HIS A:224 , LEU A:226 , ZN A:257 , HOH A:301 , HOH A:307 , HOH A:323 , HOH A:329	BINDING SITE FOR RESIDUE L04 A 256
07	CA1	UNKNOWN	ASP A:158 , GLY A:159 , GLY A:161 , VAL A:163 , ASP A:181 , GLU A:184	LIGANDS OF THE CALCIUM ION CA 259.
08	CA2	UNKNOWN	ASP A:141 , GLY A:173 , ASN A:175 , ASP A:177 , HOH A:306 , HOH A:312	LIGANDS OF THE CALCIUM ION CA 260.
09	CA3	UNKNOWN	ASP A:107 , ASP A:182 , GLU A:184 , HOH A:313 , HOH A:332	LIGANDS OF THE CALCIUM ION CA 261.
10	L04	UNKNOWN	TYR A:155 , ASN A:162 , VAL A:163 , LEU A:164 , ALA A:165 , HIS A:166 , TYR A:168 , LEU A:197 , VAL A:198 , HIS A:201 , GLU A:202 , HIS A:205 , HIS A:211 , ALA A:217 , LEU A:218 , TYR A:220 , PRO A:221 , LEU A:222 , TYR A:223 , HIS A:224 , LEU A:226 , ZN A:257	BINDING SITE FOR THE INHIBITOR L-764,004, DENOTED L04 256.
11	ZN1	UNKNOWN	HIS A:201 , HIS A:205 , HIS A:211 , L04 A:256	LIGANDS OF THE CATALYTIC (ZN 257) ZINC ION.
12	ZN2	UNKNOWN	HIS A:151 , ASP A:153 , HIS A:166 , HIS A:179	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 Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
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Chain A from PDB  Type:PROTEIN  Length:160
 aligned with MMP3_HUMAN | P08254 from UniProtKB/Swiss-Prot  Length:477

    Alignment length:160
                                   114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264
           MMP3_HUMAN   105 GIPKWRKTHLTYRIVNYTPDLPKDAVDSAVEKALKVWEEVTPLTFSRLYEGEADIMISFAVREHGDFYPFDGPGNVLAHAYAPGPGINGDAHFDDDEQWTKDTTGTNLFLVAAHEIGHSLGLFHSANTEALMYPLYHSLTDLTRFRLSQDDINGIQSLYG 264
               SCOP domains d1hfsa_ A: Stromelysin-1 (MMP-3)                                                                                                                                 SCOP domains
               CATH domains 1hfsA00 A:88-247 Collagenase (Catalytic Domain)                                                                                                                  CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeee........hhhhhhhhhhhhhhhhh....eeee.......eeeeee.................eeee........eeeee.............hhhhhhhhhhhhh............................hhhhhhhhhhh. 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)
                 1hfs A  88 GIPKWRKTHLTYRIVNYTPDLPKDAVDSAVEKALKVWEEVTPLTFSRLYEGEADIMISFAVREHGDFYPFDGPGNVLAHAYAPGPGINGDAHFDDDEQWTKDTTGTNLFLVAAHEIGHSLGLFHSANTEALMYPLYHSLTDLTRFRLSQDDINGIQSLYG 247
                                    97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247

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 (0, 0)

Gene Ontology (21, 21)

Asymmetric 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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