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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF MMP-12 IN COMPLEX WITH A SELECTIVE SUGAR-CONJUGATED TRIAZOLE-LINKED CARBOXYLATE CHELATING WATER-SOLUBLE INHIBITOR (DC24).
 
Authors :  E. A. Stura, L. Rosalia, D. Cuffaro, L. Tepshi, L. Ciccone, A. Rossello
Date :  09 Feb 16  (Deposition) - 06 Jul 16  (Release) - 17 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (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
    Cell: MACROPHAGE
    Chains: A, B, C, D
    EC Number: 3.4.24.65
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Cell Line: DE3 STAR
    Expression System Taxid: 562
    Expression System Variant: BL21
    Fragment: UNP RESIDUES 106-263
    Gene: MMP12, HME
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: MME,MACROPHAGE ELASTASE,HME,MATRIX METALLOPROTEINASE-12,MMP- 12

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 28)

Asymmetric Unit (6, 28)
No.NameCountTypeFull Name
1CA12Ligand/IonCALCIUM ION
2DMS1Ligand/IonDIMETHYL SULFOXIDE
3EDO1Ligand/Ion1,2-ETHANEDIOL
4PGO2Ligand/IonS-1,2-PROPANEDIOL
5V244Ligand/IonN-[([1,1'-BIPHENYL]-4-YL)SULFONYL]-N-({1-[3,4,6-TRI-O-ACETYL-2-(ACETYLAMINO)-2-DEOXY-BETA-D-GLUCOPYRANOSYL]-1H-1,2,3-TRIAZOL-4-YL}METHYL)-D-VALINE
6ZN8Ligand/IonZINC ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2DMS-1Ligand/IonDIMETHYL SULFOXIDE
3EDO-1Ligand/Ion1,2-ETHANEDIOL
4PGO1Ligand/IonS-1,2-PROPANEDIOL
5V241Ligand/IonN-[([1,1'-BIPHENYL]-4-YL)SULFONYL]-N-({1-[3,4,6-TRI-O-ACETYL-2-(ACETYLAMINO)-2-DEOXY-BETA-D-GLUCOPYRANOSYL]-1H-1,2,3-TRIAZOL-4-YL}METHYL)-D-VALINE
6ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2DMS-1Ligand/IonDIMETHYL SULFOXIDE
3EDO-1Ligand/Ion1,2-ETHANEDIOL
4PGO-1Ligand/IonS-1,2-PROPANEDIOL
5V241Ligand/IonN-[([1,1'-BIPHENYL]-4-YL)SULFONYL]-N-({1-[3,4,6-TRI-O-ACETYL-2-(ACETYLAMINO)-2-DEOXY-BETA-D-GLUCOPYRANOSYL]-1H-1,2,3-TRIAZOL-4-YL}METHYL)-D-VALINE
6ZN-1Ligand/IonZINC ION
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2DMS-1Ligand/IonDIMETHYL SULFOXIDE
3EDO1Ligand/Ion1,2-ETHANEDIOL
4PGO-1Ligand/IonS-1,2-PROPANEDIOL
5V241Ligand/IonN-[([1,1'-BIPHENYL]-4-YL)SULFONYL]-N-({1-[3,4,6-TRI-O-ACETYL-2-(ACETYLAMINO)-2-DEOXY-BETA-D-GLUCOPYRANOSYL]-1H-1,2,3-TRIAZOL-4-YL}METHYL)-D-VALINE
6ZN-1Ligand/IonZINC ION
Biological Unit 4 (3, 3)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2DMS1Ligand/IonDIMETHYL SULFOXIDE
3EDO-1Ligand/Ion1,2-ETHANEDIOL
4PGO1Ligand/IonS-1,2-PROPANEDIOL
5V241Ligand/IonN-[([1,1'-BIPHENYL]-4-YL)SULFONYL]-N-({1-[3,4,6-TRI-O-ACETYL-2-(ACETYLAMINO)-2-DEOXY-BETA-D-GLUCOPYRANOSYL]-1H-1,2,3-TRIAZOL-4-YL}METHYL)-D-VALINE
6ZN-1Ligand/IonZINC ION

(-) Sites  (28, 28)

Asymmetric Unit (28, 28)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:179 , ILE A:180 , LEU A:181 , ALA A:182 , HIS A:183 , LEU A:214 , THR A:215 , HIS A:218 , GLN A:219 , HIS A:222 , HIS A:228 , VAL A:235 , PHE A:237 , PRO A:238 , THR A:239 , TYR A:240 , ZN A:302 , HOH A:460 , HOH A:462 , HOH A:477 , HOH A:478 , GLU B:128 , ARG B:135binding site for residue V24 A 301
02AC2SOFTWAREHIS A:218 , HIS A:222 , HIS A:228 , V24 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:403binding site for residue CA A 304
05AC5SOFTWAREASP A:124 , GLU A:199 , GLU A:201 , HOH A:459binding 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
07AC7SOFTWARETYR A:132 , THR A:205 , PHE A:213 , ILE A:245 , HOH A:447 , HOH A:468binding site for residue PGO A 307
08AC8SOFTWAREGLU A:128 , ASP A:131 , GLY B:179 , ILE B:180 , LEU B:181 , ALA B:182 , HIS B:183 , LEU B:214 , THR B:215 , HIS B:218 , GLN B:219 , HIS B:222 , HIS B:228 , VAL B:235 , PHE B:237 , PRO B:238 , THR B:239 , TYR B:240 , ZN B:302 , HOH B:645 , HOH B:647binding site for residue V24 B 301
09AC9SOFTWAREHIS B:218 , HIS B:222 , HIS B:228 , V24 B:301binding site for residue ZN B 302
10AD1SOFTWAREHIS B:168 , ASP B:170 , HIS B:183 , HIS B:196binding site for residue ZN B 303
11AD2SOFTWAREASP B:158 , GLY B:190 , GLY B:192 , ASP B:194 , HOH B:612 , HOH B:632binding site for residue CA B 304
12AD3SOFTWAREASP B:124 , GLU B:199 , GLU B:201 , HOH B:660 , HOH B:668binding site for residue CA B 305
13AD4SOFTWAREASP B:175 , GLY B:176 , GLY B:178 , ILE B:180 , ASP B:198 , GLU B:201binding site for residue CA B 306
14AD5SOFTWAREHIS C:172 , ILE C:180 , LEU C:181 , ALA C:182 , HIS C:183 , LEU C:214 , HIS C:218 , GLN C:219 , HIS C:222 , HIS C:228 , VAL C:235 , PHE C:237 , PRO C:238 , THR C:239 , TYR C:240 , ZN C:302 , HOH C:402 , HOH C:456 , HOH C:461 , HOH C:462 , PRO D:232binding site for residue V24 C 301
15AD6SOFTWAREHIS C:218 , HIS C:222 , HIS C:228 , V24 C:301binding site for residue ZN C 302
16AD7SOFTWAREHIS C:168 , ASP C:170 , HIS C:183 , HIS C:196binding site for residue ZN C 303
17AD8SOFTWAREASP C:158 , GLY C:190 , GLY C:192 , ASP C:194 , HOH C:424 , HOH C:452binding site for residue CA C 304
18AD9SOFTWAREASP C:124 , GLU C:199 , GLU C:201 , HOH C:484 , HOH C:491binding site for residue CA C 305
19AE1SOFTWAREASP C:175 , GLY C:176 , GLY C:178 , ILE C:180 , ASP C:198 , GLU C:201binding site for residue CA C 306
20AE2SOFTWARETRP C:109 , ARG C:110 , GLY C:188binding site for residue EDO C 307
21AE3SOFTWARELYS C:241 , ASP D:175 , GLY D:179 , ILE D:180 , LEU D:181 , ALA D:182 , LEU D:214 , HIS D:218 , GLN D:219 , HIS D:222 , HIS D:228 , VAL D:235 , PHE D:237 , PRO D:238 , THR D:239 , TYR D:240 , ZN D:302 , DMS D:307 , HOH D:424 , HOH D:431 , HOH D:506binding site for residue V24 D 301
22AE4SOFTWAREHIS D:218 , HIS D:222 , HIS D:228 , V24 D:301binding site for residue ZN D 302
23AE5SOFTWAREHIS D:168 , ASP D:170 , HIS D:183 , HIS D:196binding site for residue ZN D 303
24AE6SOFTWAREASP D:158 , GLY D:190 , GLY D:192 , ASP D:194 , HOH D:404 , HOH D:423binding site for residue CA D 304
25AE7SOFTWAREASP D:124 , GLU D:199 , GLU D:201 , HOH D:433 , HOH D:482binding site for residue CA D 305
26AE8SOFTWAREASP D:175 , GLY D:176 , GLY D:178 , ILE D:180 , ASP D:198 , GLU D:201binding site for residue CA D 306
27AE9SOFTWAREHIS D:172 , ALA D:184 , V24 D:301binding site for residue DMS D 307
28AF1SOFTWARETYR D:132 , ALA D:133 , LYS D:136 , THR D:205 , PHE D:213 , HOH D:443 , HOH D:467binding site for residue PGO D 308

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5I2Z)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5I2Z)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5I2Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5I2Z)

(-) Exons   (0, 0)

(no "Exon" information available for 5I2Z)

(-) 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:157
                                                                                                                                                                                             
               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
                 5i2z A 107 PVWRKHYITYRINNYTPDMNREDVDYAIRKAFQVWSNVTPLKFSKINTGMADILVVFARGAHGDDHAFDGKGGILAHAFGPGSGIGGDAHFDEDEFWTTHSGGTNLFLTAVHQIGHSLGLGHSSDPKAVMFPTYKYVDINTFRLSADDIRGIQSLYG 263
                                   116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       


Chain B 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.....eehhhhhhhhhhhhhh.........................hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5i2z B 107 PVWRKHYITYRINNYTPDMNREDVDYAIRKAFQVWSNVTPLKFSKINTGMADILVVFARGAHGDDHAFDGKGGILAHAFGPGSGIGGDAHFDEDEFWTTHSGGTNLFLTAVHQIGHSLGLGHSSDPKAVMFPTYKYVDINTFRLSADDIRGIQSLYG 263
                                   116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       


Chain C 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.....eehhhhhhhhhhhhhh..................hhhhh..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5i2z C 107 PVWRKHYITYRINNYTPDMNREDVDYAIRKAFQVWSNVTPLKFSKINTGMADILVVFARGAHGDDHAFDGKGGILAHAFGPGSGIGGDAHFDEDEFWTTHSGGTNLFLTAVHQIGHSLGLGHSSDPKAVMFPTYKYVDINTFRLSADDIRGIQSLYG 263
                                   116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       


Chain D from PDB  Type:PROTEIN  Length:156
                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeee.......hhhhhhhhhhhhhhhhhh....eeee.......eeeeee.................eee..........eeee....ee.....eehhhhhhhhhhhhh...................hhhhh..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5i2z D 108 VWRKHYITYRINNYTPDMNREDVDYAIRKAFQVWSNVTPLKFSKINTGMADILVVFARGAHGDDHAFDGKGGILAHAFGPGSGIGGDAHFDEDEFWTTHSGGTNLFLTAVHQIGHSLGLGHSSDPKAVMFPTYKYVDINTFRLSADDIRGIQSLYG 263
                                   117       127       137       147       157       167       177       187       197       207       217       227       237       247       257
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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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5I2Z)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5I2Z)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5I2Z)

(-) Gene Ontology  (21, 21)

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  MMP12_HUMAN | P39900
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 Related Entries

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

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 5i0l 5i3m 5i43 5i4o 5l79 5l7f 5lab

(-) Related Entries Specified in the PDB File

5i12 MMP-9 WITH RELATED LIGAND
5iol SAME PROTEIN WITH RELATED LIGAND