4JA1 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF MMP3 COMPLEXED WITH A PLATINUM-BASED INHIBITOR

Authors :   B. D. Belviso, F. Arnesano, V. Calderone, R. Caliandro, G. Natile, D. Si

Date :   18 Feb 13 (Deposition) - 27 Feb 13 (Release) - 05 Jun 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.96

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

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

Reference :   B. D. Belviso, R. Caliandro, D. Siliqi, V. Calderone, F. Arnesano, G. Natile
Structure Of Matrix Metalloproteinase-3 With A Platinum-Based Inhibitor.
Chem. Commun. (Camb. ) V. 49 5492 2013
PubMed-ID: 23660647 | Reference-DOI: 10.1039/C3CC41278D

Molecule 1 - STROMELYSIN-1
	Chains	:	A, B
	EC Number	:	3.4.24.17
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	CATALYTIC DOMAIN
	Gene	:	MMP3, STMY1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	SL-1, MATRIX METALLOPROTEINASE-3, MMP-3, TRANSIN-1

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 18)

No.	Name	Count	Type	Full Name
1	CA	6	Ligand/Ion	CALCIUM ION
2	CL	4	Ligand/Ion	CHLORIDE ION
3	NGH	1	Ligand/Ion	N-ISOBUTYL-N-[4-METHOXYPHENYLSULFONYL]GLYCYL HYDROXAMICACID
4	PT	3	Ligand/Ion	PLATINUM (II) ION
5	ZN	4	Ligand/Ion	ZINC ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	NGH	-1	Ligand/Ion	N-ISOBUTYL-N-[4-METHOXYPHENYLSULFONYL]GLYCYL HYDROXAMICACID
4	PT	-1	Ligand/Ion	PLATINUM (II) ION
5	ZN	-1	Ligand/Ion	ZINC ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CA	-1	Ligand/Ion	CALCIUM ION
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	NGH	1	Ligand/Ion	N-ISOBUTYL-N-[4-METHOXYPHENYLSULFONYL]GLYCYL HYDROXAMICACID
4	PT	-1	Ligand/Ion	PLATINUM (II) ION
5	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (18, 18)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:201 , HIS A:205 , HIS A:211 , THR B:255	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:401 , HOH A:443	BINDING SITE FOR RESIDUE CA A 304
05	AC5	SOFTWARE	ASP A:107 , ASP A:182 , GLU A:184 , HOH A:405 , HOH A:415	BINDING SITE FOR RESIDUE CA A 305
06	AC6	SOFTWARE	GLU A:139 , MET A:143 , CL A:307 , HOH A:444	BINDING SITE FOR RESIDUE PT A 306
07	AC7	SOFTWARE	ALA A:140 , MET A:143 , PT A:306	BINDING SITE FOR RESIDUE CL A 307
08	AC8	SOFTWARE	HIS B:201 , HIS B:205 , HIS B:211 , NGH B:306	BINDING SITE FOR RESIDUE ZN B 301
09	AC9	SOFTWARE	HIS B:151 , ASP B:153 , HIS B:166 , HIS B:179	BINDING SITE FOR RESIDUE ZN B 302
10	BC1	SOFTWARE	ASP B:158 , GLY B:159 , GLY B:161 , VAL B:163 , ASP B:181 , GLU B:184	BINDING SITE FOR RESIDUE CA B 303
11	BC2	SOFTWARE	ASP B:141 , GLY B:173 , ASN B:175 , ASP B:177 , HOH B:402 , HOH B:404	BINDING SITE FOR RESIDUE CA B 304
12	BC3	SOFTWARE	ASP B:107 , ASP B:182 , GLU B:184 , HOH B:444 , HOH B:454	BINDING SITE FOR RESIDUE CA B 305
13	BC4	SOFTWARE	ASN B:162 , VAL B:163 , LEU B:164 , ALA B:165 , HIS B:201 , GLU B:202 , HIS B:205 , HIS B:211 , PRO B:221 , TYR B:223 , ZN B:301 , HOH B:437	BINDING SITE FOR RESIDUE NGH B 306
14	BC5	SOFTWARE	GLU B:139 , MET B:143 , CL B:309 , HOH B:440	BINDING SITE FOR RESIDUE PT B 307
15	BC6	SOFTWARE	HIS B:224 , CL B:310 , CL B:311 , HOH B:420	BINDING SITE FOR RESIDUE PT B 308
16	BC7	SOFTWARE	MET B:143 , PT B:307	BINDING SITE FOR RESIDUE CL B 309
17	BC8	SOFTWARE	TYR B:223 , HIS B:224 , PT B:308 , CL B:311 , HOH B:420	BINDING SITE FOR RESIDUE CL B 310
18	BC9	SOFTWARE	GLY A:88 , HIS B:224 , PT B:308 , CL B:310 , HOH B:420	BINDING SITE FOR RESIDUE CL B 311

(no "SS Bond" information available for 4JA1)

Asymmetric Unit

No.	Residues
1	Leu A:226	-	Thr A:227
2	Thr B:227	-	Asp B:228

(no "SAP(SNP)/Variant" information available for 4JA1)

(no "PROSITE Motif" information available for 4JA1)

(no "Exon" information available for 4JA1)

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:168
                                                                                                                                                                                                        
               SCOP domains d4ja1a_ A: Stromelysin-1 (MMP-3)                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ 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 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ja1 A  83 FRTFPGIPKWRKTHLTYRIVNYTPDLPKDAVDSAVEKALKVWEEVTPLTFSRLYEGEADIMISFAVREHGDFYPFDGPGNVLAHAYAPGPGINGDAHFDDDEQWTKDTTGTNLFLVAAHEIGHSLGLFHSANTEALMYPLYHSLTDLTRFRLSQDDINGIQSLYGPPP 250
                                    92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242

Chain B from PDB  Type:PROTEIN  Length:167
                                                                                                                                                                                                       
               SCOP domains d4ja1b_ B: Stromelysin-1 (MMP-3)                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee.......hhhhhhhhhhhhhhhhhh....eeee.......eeeeee.................eee..........eeee....ee.....eehhhhhhhhhhhhh...........................hhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ja1 B  89 IPKWRKTHLTYRIVNYTPDLPKDAVDSAVEKALKVWEEVTPLTFSRLYEGEADIMISFAVREHGDFYPFDGPGNVLAHAYAPGPGINGDAHFDDDEQWTKDTTGTNLFLVAAHEIGHSLGLFHSANTEALMYPLYHSLTDLTRFRLSQDDINGIQSLYGPPPDSPET 255
                                    98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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)

1a	d4ja1a_	A:
1b	d4ja1b_	B:

(no "CATH Domain" information available for 4JA1)

(no "Pfam Domain" information available for 4JA1)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Leu A:226 - Thr A:227	[ RasMol ]
		Thr B:227 - Asp B:228	[ RasMol ]

Biological Units
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		Biological Unit 2	[ Jena3D ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 18)

Sites (18, 18)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

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SCOP Domains (1, 2)

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Gene Ontology (21, 21)

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