1CIZ - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   X-RAY STRUCTURE OF HUMAN STROMELYSIN CATALYTIC DOMAIN COMPLEXES WITH NON-PEPTIDE INHIBITORS: IMPLICATION FOR INHIBITOR SELECTIVITY

Authors :   A. G. Pavlovsky, M. G. Williams, Q. -Z. Ye, D. F. Ortwine, C. F. Purchase A. D. White, V. Dhanaraj, B. D. Roth, L. L. Johnson, D. Hupe, C. Humblet, T. L. Blundell

Date :   06 Apr 99 (Deposition) - 01 Sep 99 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.64

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

Keywords :   Matrix Metalloproteinase, Mmp-3, Non-Peptide Inhibitor, Metalloproteinase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. G. Pavlovsky, M. G. Williams, Q. Z. Ye, D. F. Ortwine, C. F. Purchase 2Nd. , A. D. White, V. Dhanaraj, B. D. Roth, L. L. Johnson D. Hupe, C. Humblet, T. L. Blundell
X-Ray Structure Of Human Stromelysin Catalytic Domain Complexed With Nonpeptide Inhibitors: Implications For Inhibitor Selectivity.
Protein Sci. V. 8 1455 1999
PubMed-ID: 10422833

Molecule 1 - PROTEIN (STROMELYSIN-1)
	Cell Line	:	FIBROBLAST
	Chains	:	A
	EC Number	:	3.4.24.17
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEMEX-1
	Expression System Taxid	:	562
	Fragment	:	CATALYTIC DOMAIN
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	MATRIX METALLOPROTEINASE-3

		1
Asymmetric Unit	:	A
Biological Unit 1 (1x)	:	A
Biological Unit 2 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 7)

No.	Name	Count	Type	Full Name
1	CA	3	Ligand/Ion	CALCIUM ION
2	DPS	1	Ligand/Ion	3-(1H-INDOL-3-YL)-2-[4-(4-PHENYL-PIPERIDIN-1-YL)-BENZENESULFONYLAMINO]-PROPIONIC ACID
3	SO4	1	Ligand/Ion	SULFATE ION
4	ZN	2	Ligand/Ion	ZINC ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	DPS	1	Ligand/Ion	3-(1H-INDOL-3-YL)-2-[4-(4-PHENYL-PIPERIDIN-1-YL)-BENZENESULFONYLAMINO]-PROPIONIC ACID
3	SO4	1	Ligand/Ion	SULFATE ION
4	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (2, 4)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	DPS	2	Ligand/Ion	3-(1H-INDOL-3-YL)-2-[4-(4-PHENYL-PIPERIDIN-1-YL)-BENZENESULFONYLAMINO]-PROPIONIC ACID
3	SO4	2	Ligand/Ion	SULFATE ION
4	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:201 , HIS A:205 , HIS A:211 , DPS A:307	BINDING SITE FOR RESIDUE ZN A 301
02	AC2	SOFTWARE	HIS A:151 , ASP A:153 , HIS A:166 , HIS A:179	BINDING SITE FOR RESIDUE ZN A 302
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 303
04	AC4	SOFTWARE	ASP A:141 , GLY A:173 , ASN A:175 , ASP A:177 , HOH A:403 , HOH A:404	BINDING SITE FOR RESIDUE CA A 304
05	AC5	SOFTWARE	ASP A:107 , ASP A:182 , GLU A:184 , HOH A:401	BINDING SITE FOR RESIDUE CA A 305
06	AC6	SOFTWARE	PRO A:109 , LYS A:110 , HOH A:446 , HOH A:516	BINDING SITE FOR RESIDUE SO4 A 306
07	AC7	SOFTWARE	LEU A:164 , ALA A:165 , HIS A:201 , GLU A:202 , HIS A:205 , PHE A:210 , HIS A:211 , ALA A:217 , LEU A:218 , TYR A:220 , PRO A:221 , LEU A:222 , TYR A:223 , HIS A:224 , ZN A:301 , HOH A:471 , HOH A:488	BINDING SITE FOR RESIDUE DPS A 307
08	CA1	AUTHOR	ASP A:158 , GLY A:159 , GLY A:161 , VAL A:163 , ASP A:181 , GLU A:184	CA1 IS THE FIRST CALCIUM BINDING SITE.
09	CA2	AUTHOR	ASP A:141 , GLY A:173 , ASN A:175 , ASP A:177 , HOH A:403 , HOH A:404	CA2 IS THE SECOND CALCIUM BINDING SITE.
10	CA3	AUTHOR	ASP A:107 , ASP A:182 , GLU A:184 , HOH A:401	CA1 IS THE THIRD CALCIUM BINDING SITE.
11	INH	AUTHOR	DPS A:307 , ZN A:301 , ZN A:302 , CA A:303	NULL
12	ZN1	AUTHOR	CA A:304 , CA A:305 , HIS A:211 , DPS A:307	ZN1 IS THE CATALYTIC ZINC BINDING SITE.
13	ZN2	AUTHOR	HIS A:151 , ASP A:153 , HIS A:166 , HIS A:179	ZN1 IS THE STRUCTURAL ZINC BINDING SITE.

(no "SS Bond" information available for 1CIZ)

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

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

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZINC_PROTEASE	PS00142	Neutral zinc metallopeptidases, zinc-binding region signature.	MMP3_HUMAN	215-224	1	A:198-207

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZINC_PROTEASE	PS00142	Neutral zinc metallopeptidases, zinc-binding region signature.	MMP3_HUMAN	215-224	1	A:198-207

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ZINC_PROTEASE	PS00142	Neutral zinc metallopeptidases, zinc-binding region signature.	MMP3_HUMAN	215-224	2	A:198-207

Asymmetric Unit (5, 5)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000299855	1a	ENSE00002171374	chr11:102714534-102714173	362	MMP3_HUMAN	1-35	35	0	-	-
1.2	ENST00000299855	2	ENSE00001105428	chr11:102713647-102713403	245	MMP3_HUMAN	36-117	82	1	A:83-100	18
1.3	ENST00000299855	3	ENSE00001642002	chr11:102713310-102713162	149	MMP3_HUMAN	117-167	51	1	A:100-150	51
1.4b	ENST00000299855	4b	ENSE00001105420	chr11:102713010-102712885	126	MMP3_HUMAN	167-209	43	1	A:150-192	43
1.5	ENST00000299855	5	ENSE00001657829	chr11:102711324-102711160	165	MMP3_HUMAN	209-264	56	1	A:192-247	56
1.6	ENST00000299855	6	ENSE00001105427	chr11:102710983-102710839	145	MMP3_HUMAN	264-312	49	1	A:247-250	4
1.7	ENST00000299855	7	ENSE00001105439	chr11:102709974-102709841	134	MMP3_HUMAN	312-357	46	0	-	-
1.8	ENST00000299855	8	ENSE00001801971	chr11:102709441-102709282	160	MMP3_HUMAN	357-410	54	0	-	-
1.9	ENST00000299855	9	ENSE00001105448	chr11:102708132-102708029	104	MMP3_HUMAN	410-445	36	0	-	-
1.11	ENST00000299855	11	ENSE00001292630	chr11:102706957-102706532	426	MMP3_HUMAN	445-477	33	0	-	-

Asymmetric Unit

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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:168
 aligned with MMP3_HUMAN | P08254 from UniProtKB/Swiss-Prot  Length:477

    Alignment length:168
                                   109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259        
           MMP3_HUMAN   100 FRTFPGIPKWRKTHLTYRIVNYTPDLPKDAVDSAVEKALKVWEEVTPLTFSRLYEGEADIMISFAVREHGDFYPFDGPGNVLAHAYAPGPGINGDAHFDDDEQWTKDTTGTNLFLVAAHEIGHSLGLFHSANTEALMYPLYHSLTDLTRFRLSQDDINGIQSLYGPPP 267
               SCOP domains d1ciza_ A: Stromelysin-1 (MMP-3)                                                                                                                                         SCOP domains
               CATH domains 1cizA00 A:83-250 Collagenase (Catalytic Domain)                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............eeeeee........hhhhhhhhhhhhhhhhhh...eeee.......eeeeee.................eee..........eeee.............hhhhhhhhhhhhh.....................hhh....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 ------------------------------------------------------1.6  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)
                 1ciz A  83 FRTFPGIPKWRKTHLTYRIVNYTPDLPKDAVDSAVEKALKVWEEVTPLTFSRLYEGEADIMISFAVREHGDFYPFDGPGNVLAHAYAPGPGINGDAHFDDDEQWTKDTTGTNLFLVAAHEIGHSLGLFHSANTEALMYPLYHSLTDLTRFRLSQDDINGIQSLYGPPP 250
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242

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	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(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

)

Organisms( (-)

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Class: Alpha and beta proteins (a+b) (23004)

Fold: Zincin-like (701)

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

Family: Matrix metalloproteases, catalytic domain (199)

Protein domain: Stromelysin-1 (MMP-3) (40)

Human (Homo sapiens), fibroblast [TaxId: 9606] (40)

d1ciza_

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Alpha Beta (26913)

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

Topology: Collagenase (Catalytic Domain) (236)

Homologous Superfamily: Collagenase (Catalytic Domain) (234)

Human (Homo sapiens) (153)

1cizA00

A:83-250

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

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

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 7)

Sites (13, 13)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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Exons (5, 5)

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