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(-) Description

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

(-) Compounds

Molecule 1 - STROMELYSIN-1
    ChainsA, B
    EC Number3.4.24.17
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentCATALYTIC DOMAIN
    GeneMMP3, STMY1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymSL-1, MATRIX METALLOPROTEINASE-3, MMP-3, TRANSIN-1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 18)

Asymmetric Unit (5, 18)
No.NameCountTypeFull Name
1CA6Ligand/IonCALCIUM ION
2CL4Ligand/IonCHLORIDE ION
3NGH1Ligand/IonN-ISOBUTYL-N-[4-METHOXYPHENYLSULFONYL]GLYCYL HYDROXAMICACID
4PT3Ligand/IonPLATINUM (II) ION
5ZN4Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3NGH-1Ligand/IonN-ISOBUTYL-N-[4-METHOXYPHENYLSULFONYL]GLYCYL HYDROXAMICACID
4PT-1Ligand/IonPLATINUM (II) ION
5ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2CL-1Ligand/IonCHLORIDE ION
3NGH1Ligand/IonN-ISOBUTYL-N-[4-METHOXYPHENYLSULFONYL]GLYCYL HYDROXAMICACID
4PT-1Ligand/IonPLATINUM (II) ION
5ZN-1Ligand/IonZINC ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:201 , HIS A:205 , HIS A:211 , THR B:255BINDING SITE FOR RESIDUE ZN A 301
02AC2SOFTWAREHIS A:151 , ASP A:153 , HIS A:166 , HIS A:179BINDING SITE FOR RESIDUE ZN A 302
03AC3SOFTWAREASP A:158 , GLY A:159 , GLY A:161 , VAL A:163 , ASP A:181 , GLU A:184BINDING SITE FOR RESIDUE CA A 303
04AC4SOFTWAREASP A:141 , GLY A:173 , ASN A:175 , ASP A:177 , HOH A:401 , HOH A:443BINDING SITE FOR RESIDUE CA A 304
05AC5SOFTWAREASP A:107 , ASP A:182 , GLU A:184 , HOH A:405 , HOH A:415BINDING SITE FOR RESIDUE CA A 305
06AC6SOFTWAREGLU A:139 , MET A:143 , CL A:307 , HOH A:444BINDING SITE FOR RESIDUE PT A 306
07AC7SOFTWAREALA A:140 , MET A:143 , PT A:306BINDING SITE FOR RESIDUE CL A 307
08AC8SOFTWAREHIS B:201 , HIS B:205 , HIS B:211 , NGH B:306BINDING SITE FOR RESIDUE ZN B 301
09AC9SOFTWAREHIS B:151 , ASP B:153 , HIS B:166 , HIS B:179BINDING SITE FOR RESIDUE ZN B 302
10BC1SOFTWAREASP B:158 , GLY B:159 , GLY B:161 , VAL B:163 , ASP B:181 , GLU B:184BINDING SITE FOR RESIDUE CA B 303
11BC2SOFTWAREASP B:141 , GLY B:173 , ASN B:175 , ASP B:177 , HOH B:402 , HOH B:404BINDING SITE FOR RESIDUE CA B 304
12BC3SOFTWAREASP B:107 , ASP B:182 , GLU B:184 , HOH B:444 , HOH B:454BINDING SITE FOR RESIDUE CA B 305
13BC4SOFTWAREASN 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:437BINDING SITE FOR RESIDUE NGH B 306
14BC5SOFTWAREGLU B:139 , MET B:143 , CL B:309 , HOH B:440BINDING SITE FOR RESIDUE PT B 307
15BC6SOFTWAREHIS B:224 , CL B:310 , CL B:311 , HOH B:420BINDING SITE FOR RESIDUE PT B 308
16BC7SOFTWAREMET B:143 , PT B:307BINDING SITE FOR RESIDUE CL B 309
17BC8SOFTWARETYR B:223 , HIS B:224 , PT B:308 , CL B:311 , HOH B:420BINDING SITE FOR RESIDUE CL B 310
18BC9SOFTWAREGLY A:88 , HIS B:224 , PT B:308 , CL B:310 , HOH B:420BINDING SITE FOR RESIDUE CL B 311

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4JA1)

(-) 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: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)
    → 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)

Asymmetric Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (21, 21)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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        MMP3_HUMAN | P082541b3d 1b8y 1biw 1bm6 1bqo 1c3i 1c8t 1caq 1ciz 1cqr 1d5j 1d7x 1d8f 1d8m 1g05 1g49 1g4k 1hfs 1hy7 1m1w 1oo9 1qia 1qic 1slm 1sln 1uea 1ums 1umt 1usn 2d1o 2jnp 2jt5 2jt6 2srt 2usn 3ohl 3oho 3usn 4dpe 4g9l

(-) Related Entries Specified in the PDB File

4dpe