1UTZ - JenaLib

Title :   CRYSTAL STRUCTURE OF MMP-12 COMPLEXED TO (2R)-3-({[4-[(PYRI DIN-4-YL)PHENYL]-THIEN-2-YL}CARBOXAMIDO)(PHENYL)PROPANOIC ACID

Authors :   R. Morales, S. Perrier, J. M. Florent, J. Beltra, S. Dufour, I. De Mendez, P. Manceau, A. Tertre, F. Moreau, D. Compere, A. C. Dublanchet, M. O'Gara

Date :   12 Dec 03 (Deposition) - 15 Dec 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Macrophage Metalloelastase, Non-Zinc Chelator, Mmp-12, Mmp Inhibitor, Hydrolase, Metalloprotease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Morales, S. Perrier, J. M. Florent, J. Beltra, S. Dufour, I. De Mendez, P. Manceau, A. Tertre, F. Moreau, D. Compere, A. C. Dublanchet, M. O'Gara
Crystal Structures Of Novel Non-Peptidic, Non-Zinc Chelating Inhibitors Bound To Mmp-12
J. Mol. Biol. V. 341 1063 2004
PubMed-ID: 15289103 | Reference-DOI: 10.1016/J.JMB.2004.06.039

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 13)

Sites (13, 13)

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:218 , HIS A:222 , HIS A:228 , HAE A:1267	BINDING SITE FOR RESIDUE ZN A1268
02	AC2	SOFTWARE	HIS A:168 , ASP A:170 , HIS A:183 , HIS A:196	BINDING SITE FOR RESIDUE ZN A1269
03	AC3	SOFTWARE	ASP A:175 , GLY A:176 , GLY A:178 , ILE A:180 , ASP A:198 , GLU A:201	BINDING SITE FOR RESIDUE CA A1270
04	AC4	SOFTWARE	ASP A:124 , GLU A:199 , GLU A:201	BINDING SITE FOR RESIDUE CA A1271
05	AC5	SOFTWARE	HIS B:218 , HIS B:222 , HIS B:228 , HAE B:1266	BINDING SITE FOR RESIDUE ZN B1267
06	AC6	SOFTWARE	HIS B:168 , ASP B:170 , HIS B:183 , HIS B:196	BINDING SITE FOR RESIDUE ZN B1268
07	AC7	SOFTWARE	ASP B:175 , GLY B:176 , GLY B:178 , ILE B:180 , ASP B:198 , GLU B:201	BINDING SITE FOR RESIDUE CA B1269
08	AC8	SOFTWARE	ASP B:124 , GLU B:199 , GLU B:201	BINDING SITE FOR RESIDUE CA B1270
09	AC9	SOFTWARE	GLY A:179 , ILE A:180 , LEU A:181 , ALA A:182 , HIS A:218 , GLU A:219 , ALA A:234 , VAL A:235 , PHE A:237 , PRO A:238 , THR A:239 , TYR A:240 , LYS A:241 , PF3 A:1266 , HAE A:1267 , HOH A:2069 , HOH A:2070 , SER B:229 , PRO B:238	BINDING SITE FOR RESIDUE PF3 A1265
10	BC1	SOFTWARE	SER A:230 , PHE A:237 , PRO A:238 , THR A:239 , PF3 A:1265 , ASP B:175 , LYS B:177 , GLY B:178 , GLY B:179 , PHE B:202 , HIS B:206 , GLY B:208 , GLY B:209 , PRO B:238 , PF3 B:1265	BINDING SITE FOR RESIDUE PF3 A1266
11	BC2	SOFTWARE	ALA A:182 , HIS A:183 , HIS A:218 , GLU A:219 , HIS A:222 , HIS A:228 , PF3 A:1265 , ZN A:1268 , HOH A:2071 , HOH A:2072	BINDING SITE FOR RESIDUE HAE A1267
12	BC3	SOFTWARE	HIS A:228 , SER A:229 , PF3 A:1266 , GLY B:179 , ILE B:180 , LEU B:181 , ALA B:182 , LEU B:214 , HIS B:218 , GLU B:219 , ALA B:234 , VAL B:235 , PHE B:237 , PRO B:238 , THR B:239 , TYR B:240 , LYS B:241 , HAE B:1266 , HOH B:2046 , HOH B:2057 , HOH B:2058 , HOH B:2059	BINDING SITE FOR RESIDUE PF3 B1265
13	BC4	SOFTWARE	ALA B:182 , HIS B:183 , HIS B:218 , GLU B:219 , HIS B:222 , HIS B:228 , PF3 B:1265 , ZN B:1267 , HOH B:2059	BINDING SITE FOR RESIDUE HAE B1266

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

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:159
 aligned with MMP12_HUMAN | P39900 from UniProtKB/Swiss-Prot  Length:470

    Alignment length:159
                                   115       125       135       145       155       165       175       185       195       205       215       225       235       245       255         
          MMP12_HUMAN   106 GPVWRKHYITYRINNYTPDMNREDVDYAIRKAFQVWSNVTPLKFSKINTGMADILVVFARGAHGDFHAFDGKGGILAHAFGPGSGIGGDAHFDEDEFWTTHSGGTNLFLTAVHEIGHSLGLGHSSDPKAVMFPTYKYVDINTFRLSADDIRGIQSLYGD 264
               SCOP domains d1utza_ A: Macrophage elastase (MMP-12)                                                                                                                         SCOP domains
               CATH domains 1utzA00 A:106-264 Collagenase (Catalytic Domain)                                                                                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee.......hhhhhhhhhhhhhhhhhh....eeee.......eeeeee.................eee..........eeee....ee.....eehhhhhhhhhhhhh...................hhhhh..hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------ZINC_PROTE---------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1utz A 106 GPVWRKHYITYRINNYTPDMNREDVDYAIRKAFQVWSNVTPLKFSKINTGMADILVVFARGAHGDFHAFDGKGGILAHAFGPGSGIGGDAHFDEDEFWTTHSGGTNLFLTAVHEIGHSLGLGHSSDPKAVMFPTYKYVDINTFRLSADDIRGIQSLYGD 264
                                   115       125       135       145       155       165       175       185       195       205       215       225       235       245       255

Chain B from PDB  Type:PROTEIN  Length:159
 aligned with MMP12_HUMAN | P39900 from UniProtKB/Swiss-Prot  Length:470

    Alignment length:159
                                   115       125       135       145       155       165       175       185       195       205       215       225       235       245       255         
          MMP12_HUMAN   106 GPVWRKHYITYRINNYTPDMNREDVDYAIRKAFQVWSNVTPLKFSKINTGMADILVVFARGAHGDFHAFDGKGGILAHAFGPGSGIGGDAHFDEDEFWTTHSGGTNLFLTAVHEIGHSLGLGHSSDPKAVMFPTYKYVDINTFRLSADDIRGIQSLYGD 264
               SCOP domains d1utzb_ B: Macrophage elastase (MMP-12)                                                                                                                         SCOP domains
               CATH domains 1utzB00 B:106-264 Collagenase (Catalytic Domain)                                                                                                                CATH domains
           Pfam domains (1) --Peptidase_M10-1utzB01 B:108-263                                                                                                                             - Pfam domains (1)
           Pfam domains (2) --Peptidase_M10-1utzB02 B:108-263                                                                                                                             - Pfam domains (2)
         Sec.struct. author .......eeeeee.......hhhhhhhhhhhhhhhhhh....eeee.......eeeeee.................eee..........eeee....ee.....eehhhhhhhhhhhhh..........................hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------ZINC_PROTE---------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1utz B 106 GPVWRKHYITYRINNYTPDMNREDVDYAIRKAFQVWSNVTPLKFSKINTGMADILVVFARGAHGDFHAFDGKGGILAHAFGPGSGIGGDAHFDEDEFWTTHSGGTNLFLTAVHEIGHSLGLGHSSDPKAVMFPTYKYVDINTFRLSADDIRGIQSLYGD 264
                                   115       125       135       145       155       165       175       185       195       205       215       225       235       245       255

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, 2)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (21, 21)

Asymmetric Unit(hide GO term definitions)

Chain A,B (MMP12_HUMAN | P39900)

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: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: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:0050679	positive regulation of epithelial cell proliferation	Any process that activates or increases the rate or extent of epithelial cell proliferation.
	GO:0060054	positive regulation of epithelial cell proliferation involved in wound healing	Any process that activates or increases the rate or extent of epithelial cell proliferation, contributing to the restoration of integrity to a damaged tissue following an injury.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0042493	response to drug	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
	GO:0014070	response to organic cyclic compound	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic cyclic compound stimulus.
	GO:0042060	wound healing	The series of events that restore integrity to a damaged tissue, following an injury.
	GO:0035313	wound healing, spreading of epidermal cells	The migration of an epidermal cell along or through a wound gap that contributes to the reestablishment of a continuous epidermis.
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: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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