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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF MMP-9 IN COMPLEX WITH A SELECTIVE SUGAR-CONJUGATED ARYLSULFONAMIDE CARBOXYLATE WATER-SOLUBLE INHIBITOR (DC27).
 
Authors :  E. A. Stura, L. Rosalia, D. Cuffaro, L. Tepshi, L. Ciccone, A. Rossello
Date :  05 Feb 16  (Deposition) - 06 Jul 16  (Release) - 17 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.59
Chains :  Asym./Biol. Unit :  A
Keywords :  Inhibitor, Complex, Glycoconjugate, Metalloprotease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  E. Nuti, D. Cuffaro, F. D'Andrea, L. Rosalia, L. Tepshi, M. Fabbi, G. Carbotti, S. Ferrini, S. Santamaria, C. Camodeca, L. Ciccone, E. Orlandini, S. Nencetti, E. A. Stura, V. Dive, A. Rossello
Sugar-Based Arylsulfonamide Carboxylates As Selective And Water-Soluble Matrix Metalloproteinase-12 Inhibitors.
Chemmedchem V. 11 1626 2016
PubMed-ID: 27356908  |  Reference-DOI: 10.1002/CMDC.201600235

(-) Compounds

Molecule 1 - MATRIX METALLOPROTEINASE-9,MATRIX METALLOPROTEINASE-9
    CellNEUTROPHIL
    ChainsA
    EC Number3.4.24.35, 3.4.24.35
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentUNP RESIDUES 113-216,UNP RESIDUES 392-444,UNP RESIDUES 113- 216,UNP RESIDUES 392-444
    GeneMMP9, CLG4B
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsMMP-9 CATALYTIC DOMAIN WITHOUT FIBRONECTIN TYPE II DOMAINS
    SynonymMMP-9,92 KDA GELATINASE,92 KDA TYPE IV COLLAGENASE, GELATINASE B,GELB,MMP-9,92 KDA GELATINASE,92 KDA TYPE IV COLLAGENASE, GELATINASE B,GELB

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 9)

Asymmetric/Biological Unit (6, 9)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION
2DMS1Ligand/IonDIMETHYL SULFOXIDE
3EDO1Ligand/Ion1,2-ETHANEDIOL
4GOL1Ligand/IonGLYCEROL
5H271Ligand/Ion(2R)-2-[{(E)-2-[({(2R,3R,4R,5S,6R)-3-(ACETYLAMINO)-4,5-BIS(ACETYLOXY)-6-[(ACETYLOXY)METHYL]TETRAHYDRO-2H-PYRAN-2-YL}CARBAMOTHIOYL)AMINO]ETHENYL}(BIPHENYL-4-YLSULFONYL)AMINO]-3-METHYLBUTANOIC ACID
6ZN2Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:226 , HIS A:230 , HIS A:236 , H27 A:306binding site for residue ZN A 301
2AC2SOFTWAREHIS A:175 , ASP A:177 , HIS A:190 , HIS A:203binding site for residue ZN A 302
3AC3SOFTWAREASP A:182 , GLY A:183 , ASP A:185 , LEU A:187 , ASP A:205 , GLU A:208binding site for residue CA A 303
4AC4SOFTWAREASP A:165 , GLY A:197 , GLN A:199 , ASP A:201 , HOH A:420 , HOH A:424binding site for residue CA A 304
5AC5SOFTWAREASP A:131 , ASP A:206 , GLU A:208 , HOH A:451 , HOH A:476binding site for residue CA A 305
6AC6SOFTWARELEU A:187 , LEU A:188 , ALA A:189 , LYS A:214 , LEU A:222 , HIS A:226 , GLU A:227 , HIS A:230 , HIS A:236 , LEU A:243 , TYR A:245 , PRO A:246 , MET A:247 , ASN A:262 , HIS A:266 , ZN A:301 , GOL A:309 , HOH A:404binding site for residue H27 A 306
7AC7SOFTWAREASP A:113 , LYS A:115 , TRP A:116 , HIS A:117 , HIS A:118binding site for residue EDO A 307
8AC8SOFTWARETYR A:179 , ALA A:191binding site for residue DMS A 308
9AC9SOFTWAREPRO A:240 , GLU A:241 , ALA A:242 , ARG A:249 , THR A:251 , H27 A:306binding site for residue GOL A 309

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5I12)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5I12)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5I12)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5I12)

(-) Exons   (0, 0)

(no "Exon" information available for 5I12)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:157
                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------- 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
                 5i12 A 113 DLKWHHHNITYWIQNYSEDLPRAVIDDAFARAFALWSAVTPLTFTRVYSRDADIVIQFGVAEHGDGYPFDGKDGLLAHAFPPGPGIQGDAHFDDDELWSLGKGVGYSLFLVAAHEFGHALGLDHSSVPEALMYPMYRFTEGPPLHKDDVNGIRHLYG 269
                                   122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       

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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5I12)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5I12)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5I12)

(-) Gene Ontology  (38, 38)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        MMP9_HUMAN | P147801gkc 1gkd 1itv 1l6j 1lkg 2ovx 2ovz 2ow0 2ow1 2ow2 4h1q 4h2e 4h3x 4h82 4hma 4jij 4jqg 4wzv 4xct 5cuh 5th6 5th9

(-) Related Entries Specified in the PDB File

4hma CRYSTAL STRUCTURE OF MMP-9 CATALYTIC DOMAIN WITH A RELATED CARBOXYLATE BASED INHIBITOR
5iol MMP-12 WITH THE SAME LIGAND.