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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF MMP-12 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 :  04 Feb 16  (Deposition) - 06 Jul 16  (Release) - 16 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
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 - MACROPHAGE METALLOELASTASE
    Chains: A, B
    EC Number: 3.4.24.65
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: STAR
    Fragment: UNP RESIDUES 106-263
    Gene: MMP12, HME
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: CATALYTIC DOMAIN OF MMP-12 WITH F171D MUTATION.
    Synonym: MME,MACROPHAGE ELASTASE,HME,MATRIX METALLOPROTEINASE-12,MMP- 12
    Tissue: MACROPHAGE

 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  (7, 18)

Asymmetric Unit (7, 18)
No.NameCountTypeFull Name
1CA6Ligand/IonCALCIUM ION
2DMS1Ligand/IonDIMETHYL SULFOXIDE
3EDO3Ligand/Ion1,2-ETHANEDIOL
4H272Ligand/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
5PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
6PGO1Ligand/IonS-1,2-PROPANEDIOL
7ZN4Ligand/IonZINC ION
Biological Unit 1 (4, 4)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2DMS-1Ligand/IonDIMETHYL SULFOXIDE
3EDO1Ligand/Ion1,2-ETHANEDIOL
4H271Ligand/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
5PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
6PGO1Ligand/IonS-1,2-PROPANEDIOL
7ZN-1Ligand/IonZINC ION
Biological Unit 2 (3, 4)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2DMS1Ligand/IonDIMETHYL SULFOXIDE
3EDO2Ligand/Ion1,2-ETHANEDIOL
4H271Ligand/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
5PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
6PGO-1Ligand/IonS-1,2-PROPANEDIOL
7ZN-1Ligand/IonZINC ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREILE A:180 , LEU A:181 , ALA A:182 , HIS A:183 , LEU A:214 , HIS A:218 , GLU A:219 , HIS A:222 , HIS A:228 , VAL A:235 , PHE A:237 , PRO A:238 , TYR A:240 , ZN A:302 , HOH A:434binding site for residue H27 A 301
02AC2SOFTWAREHIS A:218 , HIS A:222 , HIS A:228 , H27 A:301binding site for residue ZN A 302
03AC3SOFTWAREHIS A:168 , ASP A:170 , HIS A:183 , HIS A:196binding site for residue ZN A 303
04AC4SOFTWAREASP A:158 , GLY A:190 , GLY A:192 , ASP A:194 , HOH A:422 , HOH A:450binding site for residue CA A 304
05AC5SOFTWAREASP A:124 , GLU A:199 , GLU A:201 , HOH A:462 , HOH A:522binding site for residue CA A 305
06AC6SOFTWAREASP A:175 , GLY A:176 , GLY A:178 , ILE A:180 , ASP A:198 , GLU A:201binding site for residue CA A 306
07AC7SOFTWAREGLY A:227 , ASP A:253binding site for residue PGO A 307
08AC8SOFTWARETRP A:109 , HIS A:112 , LYS A:177 , ASP A:200 , LEU A:261 , HOH A:522binding site for residue EDO A 308
09AC9SOFTWAREASP A:253 , ARG A:256binding site for residue PEG A 309
10AD1SOFTWAREPRO A:232 , LYS A:233 , LYS A:241 , HOH A:409 , GLY B:179 , ILE B:180 , LEU B:181 , ALA B:182 , LEU B:214 , THR B:215 , HIS B:218 , GLU B:219 , HIS B:222 , HIS B:228 , VAL B:235 , PHE B:237 , PRO B:238 , THR B:239 , ZN B:302 , EDO B:308 , DMS B:309 , HOH B:401binding site for residue H27 B 301
11AD2SOFTWAREHIS B:218 , HIS B:222 , HIS B:228 , H27 B:301binding site for residue ZN B 302
12AD3SOFTWAREHIS B:168 , ASP B:170 , HIS B:183 , HIS B:196binding site for residue ZN B 303
13AD4SOFTWAREASP B:158 , GLY B:190 , GLY B:192 , ASP B:194 , HOH B:417 , HOH B:430binding site for residue CA B 304
14AD5SOFTWAREASP B:124 , GLU B:199 , GLU B:201 , HOH B:463binding site for residue CA B 305
15AD6SOFTWAREASP B:175 , GLY B:176 , GLY B:178 , ILE B:180 , ASP B:198 , GLU B:201binding site for residue CA B 306
16AD7SOFTWAREVAL B:108 , TRP B:109 , ARG B:110binding site for residue EDO B 307
17AD8SOFTWAREILE B:180 , H27 B:301 , HOH B:404 , HOH B:464binding site for residue EDO B 308
18AD9SOFTWAREGLY B:179 , LEU B:181 , THR B:239 , TYR B:240 , H27 B:301 , HOH B:457 , HOH B:479binding site for residue DMS B 309

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5I0L)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5I0L)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5I0L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5I0L)

(-) Exons   (0, 0)

(no "Exon" information available for 5I0L)

(-) 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:158
                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- 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
                 5i0l A 106 GPVWRKHYITYRINNYTPDMNREDVDYAIRKAFQVWSNVTPLKFSKINTGMADILVVFARGAHGDDHAFDGKGGILAHAFGPGSGIGGDAHFDEDEFWTTHSGGTNLFLTAVHEIGHSLGLGHSSDPKAVMFPTYKYVDINTFRLSADDIRGIQSLYG 263
                                   115       125       135       145       155       165       175       185       195       205       215       225       235       245       255        


Chain B from PDB  Type:PROTEIN  Length:159
                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeee.......hhhhhhhhhhhhhhhhhh....eeee.......eeeeee.................eee..........eeee....ee.....eehhhhhhhhhhhhhh.........................hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5i0l B 105 MGPVWRKHYITYRINNYTPDMNREDVDYAIRKAFQVWSNVTPLKFSKINTGMADILVVFARGAHGDDHAFDGKGGILAHAFGPGSGIGGDAHFDEDEFWTTHSGGTNLFLTAVHEIGHSLGLGHSSDPKAVMFPTYKYVDINTFRLSADDIRGIQSLYG 263
                                   114       124       134       144       154       164       174       184       194       204       214       224       234       244       254
   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  (0, 0)

(no "SCOP Domain" information available for 5I0L)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5I0L)

(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (21, 21)

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 Related Entries

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UniProtKB/Swiss-Prot
        MMP12_HUMAN | P39900: 1jiz 1jk3 1os2 1os9 1rmz 1ros 1utt 1utz 1y93 1ycm 1z3j 2hu6 2jxy 2k2g 2k9c 2krj 2mlr 2mls 2n8r 2oxu 2oxw 2oxz 2poj 2w0d 2wo8 2wo9 2woa 2z2d 3ba0 3ehx 3ehy 3f15 3f16 3f17 3f18 3f19 3f1a 3lik 3lil 3lir 3ljg 3lk8 3lka 3n2u 3n2v 3nx7 3rts 3rtt 3ts4 3tsk 3uvc 4efs 4gql 4gr0 4gr3 4gr8 4guy 4h30 4h49 4h76 4h84 4i03 4ijo 5cxa 5czm 5d2b 5d3c 5i2z 5i3m 5i43 5i4o 5l79 5l7f 5lab

(-) Related Entries Specified in the PDB File

4h30 SAME PROTEIN. THE GLYCOCONJUGATE INHIBITOR IN THIS STRUCTURE SHOULD BE COMPARED WITH THE DIMERIC LIGAND IN ENTRY 4H30.
4h84 SAME PROTEIN. THE INHIBITOR IS AN GLYCOCONJUGATE OF THE INHIBITOR IN ENTRY 4H84.