1B8Y - JenaLib

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Title :   X-RAY STRUCTURE OF HUMAN STROMELYSIN CATALYTIC DOMAIN COMPLEXED WITH NON-PEPTIDE INHIBITORS: IMPLICATIONS 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 :   03 Feb 99 (Deposition) - 31 Aug 99 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Hydrolase, Matrix Metalloproteinase-3, Stromelysin-1 (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)
	Chains	:	A
	EC Number	:	3.4.24.17
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	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	IN7	1	Ligand/Ion	[4-(4-PHENYL-PIPERIDIN-1-YL)-BENZENESULFONYLAMINO]-ACETIC 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	IN7	1	Ligand/Ion	[4-(4-PHENYL-PIPERIDIN-1-YL)-BENZENESULFONYLAMINO]-ACETIC 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	IN7	2	Ligand/Ion	[4-(4-PHENYL-PIPERIDIN-1-YL)-BENZENESULFONYLAMINO]-ACETIC 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 , IN7 A:502	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:444	BINDING SITE FOR RESIDUE SO4 A 501
07	AC7	SOFTWARE	LEU A:164 , ALA A:165 , HIS A:201 , GLU A:202 , 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:406	BINDING SITE FOR RESIDUE IN7 A 502
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 OF CA 303.
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 OF CA 304.
10	CA3	AUTHOR	ASP A:107 , ASP A:182 , GLU A:184 , HOH A:401	CA3 IS THE THIRD CALCIUM BINDING SITE OF CA 305.
11	IN7	AUTHOR	IN7 A:502	IN7 IS THE BINDING SITE FOR THE DIPHENYLPIPERIDINE SULFONAMIDE INHIBITOR.
12	ZN1	AUTHOR	HIS A:201 , HIS A:205 , HIS A:211 , IN7 A:502	ZN1 IS THE CATALYTIC ZINC BINDING SITE OF ZN 301.
13	ZN2	AUTHOR	HIS A:151 , ASP A:153 , HIS A:166 , HIS A:179	ZN2 IS THE STRUCTURAL ZINC BINDING SITE OF ZN 302.

(no "SS Bond" information available for 1B8Y)

(no "Cis Peptide Bond" information available for 1B8Y)

(no "SAP(SNP)/Variant" information available for 1B8Y)

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:247-249	3
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:167
 aligned with MMP3_HUMAN | P08254 from UniProtKB/Swiss-Prot  Length:477

    Alignment length:167
                                   109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       
           MMP3_HUMAN   100 FRTFPGIPKWRKTHLTYRIVNYTPDLPKDAVDSAVEKALKVWEEVTPLTFSRLYEGEADIMISFAVREHGDFYPFDGPGNVLAHAYAPGPGINGDAHFDDDEQWTKDTTGTNLFLVAAHEIGHSLGLFHSANTEALMYPLYHSLTDLTRFRLSQDDINGIQSLYGPP 266
               SCOP domains d1b8ya_ A: Stromelysin-1 (MMP-3)                                                                                                                                        SCOP domains
               CATH domains 1b8yA00 A:83-249 Collagenase (Catalytic Domain)                                                                                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeee........hhhhhhhhhhhhhhhhhh...eeee.......eeeeee.................eee..........eeee.............hhhhhhhhhhhh......................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)
                 1b8y A  83 FRTFPGIPKWRKTHLTYRIVNYTPDLPKDAVDSAVEKALKVWEEVTPLTFSRLYEGEADIMISFAVREHGDFYPFDGPGNVLAHAYAPGPGINGDAHFDDDEQWTKDTTGTNLFLVAAHEIGHSLGLFHSANTEALMYPLYHSLTDLTRFRLSQDDINGIQSLYGPP 249
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242

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	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( (-)

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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)

d1b8ya_

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)

1b8yA00

A:83-249

(no "Pfam Domain" information available for 1B8Y)

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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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1b8y)

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	1b8y
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	3.4.24.17
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(no "Related Entries Specified in the PDB File" available for 1B8Y)

Description

Compounds

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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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