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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 CHELATOR WATER-SOLUBLE INHIBITOR (DC32).
 
Authors :  E. A. Stura, L. Rosalia, D. Cuffaro, L. Tepshi, L. Ciccone, A. Rossello
Date :  11 Feb 16  (Deposition) - 06 Jul 16  (Release) - 17 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
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 Strain: BL21
    Expression System Taxid: 562
    Expression System Variant: DE3 STAR
    Gene: MMP12, HME
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: FRAGMENT: CATALITIC SUBUNIT (UNP RESIDUES 106-263)
    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, 55)

Asymmetric Unit (6, 55)
No.NameCountTypeFull Name
167M4Ligand/Ion(2R)-2-[({1-[3-({(2R,3R,4R,5S,6R)-3-(ACETYLAMINO)-4,5-BIS(ACETYLOXY)-6-[(ACETYLOXY)METHYL]TETRAHYDRO-2H-PYRAN-2-YL}OXY)PROPYL]-1H-1,2,3-TRIAZOL-4-YL}METHYL)(BIPHENYL-4-YLSULFONYL)AMINO]-3-METHYLBUTANOIC ACID(NON-PREFERRED NAME)
2CA12Ligand/IonCALCIUM ION
3DMS2Ligand/IonDIMETHYL SULFOXIDE
4EDO23Ligand/Ion1,2-ETHANEDIOL
5PGO6Ligand/IonS-1,2-PROPANEDIOL
6ZN8Ligand/IonZINC ION
Biological Unit 1 (2, 11)
No.NameCountTypeFull Name
167M1Ligand/Ion(2R)-2-[({1-[3-({(2R,3R,4R,5S,6R)-3-(ACETYLAMINO)-4,5-BIS(ACETYLOXY)-6-[(ACETYLOXY)METHYL]TETRAHYDRO-2H-PYRAN-2-YL}OXY)PROPYL]-1H-1,2,3-TRIAZOL-4-YL}METHYL)(BIPHENYL-4-YLSULFONYL)AMINO]-3-METHYLBUTANOIC ACID(NON-PREFERRED NAME)
2CA-1Ligand/IonCALCIUM ION
3DMS-1Ligand/IonDIMETHYL SULFOXIDE
4EDO10Ligand/Ion1,2-ETHANEDIOL
5PGO-1Ligand/IonS-1,2-PROPANEDIOL
6ZN-1Ligand/IonZINC ION
Biological Unit 2 (4, 8)
No.NameCountTypeFull Name
167M1Ligand/Ion(2R)-2-[({1-[3-({(2R,3R,4R,5S,6R)-3-(ACETYLAMINO)-4,5-BIS(ACETYLOXY)-6-[(ACETYLOXY)METHYL]TETRAHYDRO-2H-PYRAN-2-YL}OXY)PROPYL]-1H-1,2,3-TRIAZOL-4-YL}METHYL)(BIPHENYL-4-YLSULFONYL)AMINO]-3-METHYLBUTANOIC ACID(NON-PREFERRED NAME)
2CA-1Ligand/IonCALCIUM ION
3DMS1Ligand/IonDIMETHYL SULFOXIDE
4EDO5Ligand/Ion1,2-ETHANEDIOL
5PGO1Ligand/IonS-1,2-PROPANEDIOL
6ZN-1Ligand/IonZINC ION
Biological Unit 3 (4, 8)
No.NameCountTypeFull Name
167M1Ligand/Ion(2R)-2-[({1-[3-({(2R,3R,4R,5S,6R)-3-(ACETYLAMINO)-4,5-BIS(ACETYLOXY)-6-[(ACETYLOXY)METHYL]TETRAHYDRO-2H-PYRAN-2-YL}OXY)PROPYL]-1H-1,2,3-TRIAZOL-4-YL}METHYL)(BIPHENYL-4-YLSULFONYL)AMINO]-3-METHYLBUTANOIC ACID(NON-PREFERRED NAME)
2CA-1Ligand/IonCALCIUM ION
3DMS1Ligand/IonDIMETHYL SULFOXIDE
4EDO2Ligand/Ion1,2-ETHANEDIOL
5PGO4Ligand/IonS-1,2-PROPANEDIOL
6ZN-1Ligand/IonZINC ION
Biological Unit 4 (3, 8)
No.NameCountTypeFull Name
167M1Ligand/Ion(2R)-2-[({1-[3-({(2R,3R,4R,5S,6R)-3-(ACETYLAMINO)-4,5-BIS(ACETYLOXY)-6-[(ACETYLOXY)METHYL]TETRAHYDRO-2H-PYRAN-2-YL}OXY)PROPYL]-1H-1,2,3-TRIAZOL-4-YL}METHYL)(BIPHENYL-4-YLSULFONYL)AMINO]-3-METHYLBUTANOIC ACID(NON-PREFERRED NAME)
2CA-1Ligand/IonCALCIUM ION
3DMS-1Ligand/IonDIMETHYL SULFOXIDE
4EDO6Ligand/Ion1,2-ETHANEDIOL
5PGO1Ligand/IonS-1,2-PROPANEDIOL
6ZN-1Ligand/IonZINC ION

(-) Sites  (55, 55)

Asymmetric Unit (55, 55)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:218 , HIS A:222 , HIS A:228 , 67M A:306binding site for residue ZN A 301
02AC2SOFTWAREHIS A:168 , ASP A:170 , HIS A:183 , HIS A:196binding site for residue ZN A 302
03AC3SOFTWAREASP A:158 , GLY A:190 , GLY A:192 , ASP A:194 , HOH A:428 , HOH A:432binding site for residue CA A 303
04AC4SOFTWAREASP A:124 , GLU A:199 , GLU A:201 , HOH A:444 , HOH A:478binding site for residue CA A 304
05AC5SOFTWAREASP A:175 , GLY A:176 , GLY A:178 , ILE A:180 , ASP A:198 , GLU A:201binding site for residue CA A 305
06AC6SOFTWAREGLY A:178 , GLY A:179 , ILE A:180 , LEU A:181 , ALA A:182 , HIS A:183 , LEU A:214 , HIS A:218 , GLN A:219 , HIS A:222 , HIS A:228 , VAL A:235 , PHE A:237 , PRO A:238 , TYR A:240 , ZN A:301 , HOH A:413 , HOH A:436 , HOH A:466 , LYS B:241binding site for residue 67M A 306
07AC7SOFTWAREASN A:246binding site for residue EDO A 307
08AC8SOFTWARELEU A:226 , ASP A:253 , ASP A:254 , HOH A:441binding site for residue EDO A 308
09AC9SOFTWAREVAL A:108 , TRP A:109 , ARG A:110binding site for residue EDO A 309
10AD1SOFTWAREASN A:153 , HOH A:412binding site for residue EDO A 310
11AD2SOFTWARELYS A:177 , SER C:260binding site for residue EDO A 311
12AD3SOFTWAREGLN A:139 , SER A:142 , LYS A:148 , PHE A:149 , HOH A:404binding site for residue EDO A 312
13AD4SOFTWAREASN A:120 , PHE A:163binding site for residue EDO A 313
14AD5SOFTWARETYR A:121 , THR A:122 , ARG A:127 , HOH A:414binding site for residue EDO A 314
15AD6SOFTWARELYS A:136 , THR A:205 , PHE A:213 , HOH A:470binding site for residue EDO A 315
16AD7SOFTWAREGLY A:166 , PHE A:174 , ASP A:175 , GLY A:176binding site for residue EDO A 316
17AD8SOFTWAREHOH A:435 , GLY B:179 , ILE B:180 , LEU B:181 , ALA B:182 , HIS B:183 , LEU B:214 , HIS B:218 , GLN B:219 , HIS B:222 , HIS B:228 , VAL B:235 , PHE B:237 , PRO B:238 , TYR B:240 , ZN B:302 , DMS B:312 , HOH B:434 , HOH B:468 , HOH B:533binding site for residue 67M B 301
18AD9SOFTWAREHIS B:218 , HIS B:222 , HIS B:228 , 67M B:301binding site for residue ZN B 302
19AE1SOFTWAREHIS B:168 , ASP B:170 , HIS B:183 , HIS B:196binding site for residue ZN B 303
20AE2SOFTWAREASP B:158 , GLY B:190 , GLY B:192 , ASP B:194 , HOH B:442 , HOH B:454binding site for residue CA B 304
21AE3SOFTWAREASP B:124 , GLU B:199 , GLU B:201 , HOH B:475 , HOH B:487binding site for residue CA B 305
22AE4SOFTWAREASP B:175 , GLY B:176 , GLY B:178 , ILE B:180 , ASP B:198 , GLU B:201binding site for residue CA B 306
23AE5SOFTWAREALA B:184 , GLY B:186 , HIS B:222 , GLY B:225 , LEU B:226binding site for residue EDO B 307
24AE6SOFTWARELYS B:241 , TYR B:242 , HOH B:449binding site for residue EDO B 308
25AE7SOFTWAREVAL B:144 , THR B:145 , PRO B:146binding site for residue EDO B 309
26AE8SOFTWARELYS B:177 , PHE B:202 , HOH B:416 , HOH B:425binding site for residue EDO B 310
27AE9SOFTWAREHOH B:455binding site for residue EDO B 311
28AF1SOFTWAREPHE B:185 , 67M B:301binding site for residue DMS B 312
29AF2SOFTWAREARG B:127binding site for residue PGO B 313
30AF3SOFTWAREGLY C:179 , 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 , TYR C:240 , ZN C:302 , DMS C:309 , PGO C:312 , HOH C:408 , HOH C:417 , HOH C:433 , HOH C:519 , HOH C:533binding site for residue 67M C 301
31AF4SOFTWAREHIS C:218 , HIS C:222 , HIS C:228 , 67M C:301binding site for residue ZN C 302
32AF5SOFTWAREHIS C:168 , ASP C:170 , HIS C:183 , HIS C:196binding site for residue ZN C 303
33AF6SOFTWAREASP C:158 , GLY C:190 , GLY C:192 , ASP C:194 , HOH C:420 , HOH C:460binding site for residue CA C 304
34AF7SOFTWAREASP C:124 , GLU C:199 , GLU C:201 , HOH C:474 , HOH C:493binding site for residue CA C 305
35AF8SOFTWAREASP C:175 , GLY C:176 , GLY C:178 , ILE C:180 , ASP C:198 , GLU C:201binding site for residue CA C 306
36AF9SOFTWAREASN C:246 , THR C:247 , HOH C:415binding site for residue EDO C 307
37AG1SOFTWARELYS C:241 , TYR C:242 , HOH C:491binding site for residue EDO C 308
38AG2SOFTWAREGLY C:179 , LEU C:181 , TYR C:240 , 67M C:301binding site for residue DMS C 309
39AG3SOFTWARELEU C:226 , GLY C:227 , SER C:229 , MET C:236 , ASP C:253 , HOH C:438binding site for residue PGO C 310
40AG4SOFTWAREASP A:200 , VAL C:108 , TRP C:109 , LEU C:261 , HOH C:411 , HOH C:477binding site for residue PGO C 311
41AG5SOFTWAREHIS C:172 , ALA C:184 , 67M C:301binding site for residue PGO C 312
42AG6SOFTWAREVAL C:108 , ARG C:110binding site for residue PGO C 313
43AG7SOFTWARELYS C:241 , GLY D:178 , GLY D:179 , ILE D:180 , LEU D:181 , ALA D:182 , HIS D:183 , LEU D:214 , HIS D:218 , GLN D:219 , HIS D:222 , HIS D:228 , VAL D:235 , PHE D:237 , PRO D:238 , TYR D:240 , ZN D:302 , EDO D:309 , HOH D:428 , HOH D:485 , HOH D:491 , HOH D:494 , HOH D:503 , HOH D:550binding site for residue 67M D 301
44AG8SOFTWAREHIS D:218 , HIS D:222 , HIS D:228 , 67M D:301binding site for residue ZN D 302
45AG9SOFTWAREHIS D:168 , ASP D:170 , HIS D:183 , HIS D:196binding site for residue ZN D 303
46AH1SOFTWAREASP D:158 , GLY D:190 , GLY D:192 , ASP D:194 , HOH D:415 , HOH D:419binding site for residue CA D 304
47AH2SOFTWAREASP D:124 , GLU D:199 , GLU D:201 , HOH D:448 , HOH D:501binding site for residue CA D 305
48AH3SOFTWAREASP D:175 , GLY D:176 , GLY D:178 , ILE D:180 , ASP D:198 , GLU D:201binding site for residue CA D 306
49AH4SOFTWAREHOH D:432binding site for residue EDO D 307
50AH5SOFTWAREHIS D:172 , ALA D:184 , PHE D:185binding site for residue EDO D 308
51AH6SOFTWAREPRO D:232 , ALA D:234 , PHE D:237 , THR D:239 , LYS D:241 , VAL D:243 , 67M D:301binding site for residue EDO D 309
52AH7SOFTWAREVAL D:108 , TRP D:109 , ARG D:110 , GLY D:188 , HOH D:440binding site for residue EDO D 310
53AH8SOFTWAREARG D:135 , PHE D:138 , GLN D:139 , PHE D:149binding site for residue EDO D 311
54AH9SOFTWAREARG D:127 , HOH D:443 , HOH D:471binding site for residue EDO D 312
55AI1SOFTWAREGLY D:225 , LEU D:226 , GLY D:227binding site for residue PGO D 313

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5I43)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly B:106 -Pro B:107

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5I43)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5I43)

(-) Exons   (0, 0)

(no "Exon" information available for 5I43)

(-) 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..................hhhhh..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5i43 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:159
                                                                                                                                                                                               
               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
                 5i43 B 105 MGPVWRKHYITYRINNYTPDMNREDVDYAIRKAFQVWSNVTPLKFSKINTGMADILVVFARGAHGDDHAFDGKGGILAHAFGPGSGIGGDAHFDEDEFWTTHSGGTNLFLTAVHQIGHSLGLGHSSDPKAVMFPTYKYVDINTFRLSADDIRGIQSLYG 263
                                   114       124       134       144       154       164       174       184       194       204       214       224       234       244       254         


Chain C 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..........................hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5i43 C 106 GPVWRKHYITYRINNYTPDMNREDVDYAIRKAFQVWSNVTPLKFSKINTGMADILVVFARGAHGDDHAFDGKGGILAHAFGPGSGIGGDAHFDEDEFWTTHSGGTNLFLTAVHQIGHSLGLGHSSDPKAVMFPTYKYVDINTFRLSADDIRGIQSLYG 263
                                   115       125       135       145       155       165       175       185       195       205       215       225       235       245       255        


Chain D 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.....eehhhhhhhhhhhhhh..................hhhhh..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5i43 D 106 GPVWRKHYITYRINNYTPDMNREDVDYAIRKAFQVWSNVTPLKFSKINTGMADILVVFARGAHGDDHAFDGKGGILAHAFGPGSGIGGDAHFDEDEFWTTHSGGTNLFLTAVHQIGHSLGLGHSSDPKAVMFPTYKYVDINTFRLSADDIRGIQSLYG 263
                                   115       125       135       145       155       165       175       185       195       205       215       225       235       245       255
   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 5I43)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5I43)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5I43)

(-) Gene Ontology  (21, 21)

Asymmetric Unit(hide GO term definitions)

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  5i43
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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 5i2z 5i3m 5i4o 5l79 5l7f 5lab

(-) Related Entries Specified in the PDB File

5i12 MMP-9
5i2z SAME PROTEIN WITH RELATED LIGAND
5i3m SAME PROTEIN WITH RELATED LIGAND
5iol SAME PROTEIN WITH RELATED LIGAND