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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF MMP-12 IN COMPLEX WITH A SELECTIVE SUGAR-CONJUGATED THIOUREA-LINKED CARBOXYLATE ZINC-CHELATOR WATER-SOLUBLE INHIBITOR (DC31).
 
Authors :  E. A. Stura, L. Rosalia, D. Cuffaro, L. Tepshi, L. Ciccone, A. Rossello
Date :  10 Feb 16  (Deposition) - 06 Jul 16  (Release) - 17 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.17
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 Taxid: 562
    Gene: MMP12, HME
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: MACROPHAGE ELASTASE
    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  (7, 32)

Asymmetric Unit (7, 32)
No.NameCountTypeFull Name
167F4Ligand/Ion(2S)-2-{[2-({[(2R,3R,4R,5S,6R)-3-(ACETYLAMINO)-4,5-DIHYDROXY-6-(HYDROXYMETHYL)TETRAHYDRO-2H-PYRAN-2-YL]CARBAMOTHIOYL}AMINO)ETHYL](BIPHENYL-4-YLSULFONYL)AMINO}-3-METHYLBUTANOIC ACID (NON-PREFERRED NAME)
2CA12Ligand/IonCALCIUM ION
3DIO3Ligand/Ion1,4-DIETHYLENE DIOXIDE
4DMS2Ligand/IonDIMETHYL SULFOXIDE
5EDO1Ligand/Ion1,2-ETHANEDIOL
6PGO2Ligand/IonS-1,2-PROPANEDIOL
7ZN8Ligand/IonZINC ION
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
167F1Ligand/Ion(2S)-2-{[2-({[(2R,3R,4R,5S,6R)-3-(ACETYLAMINO)-4,5-DIHYDROXY-6-(HYDROXYMETHYL)TETRAHYDRO-2H-PYRAN-2-YL]CARBAMOTHIOYL}AMINO)ETHYL](BIPHENYL-4-YLSULFONYL)AMINO}-3-METHYLBUTANOIC ACID (NON-PREFERRED NAME)
2CA-1Ligand/IonCALCIUM ION
3DIO-1Ligand/Ion1,4-DIETHYLENE DIOXIDE
4DMS1Ligand/IonDIMETHYL SULFOXIDE
5EDO-1Ligand/Ion1,2-ETHANEDIOL
6PGO1Ligand/IonS-1,2-PROPANEDIOL
7ZN-1Ligand/IonZINC ION
Biological Unit 2 (3, 4)
No.NameCountTypeFull Name
167F1Ligand/Ion(2S)-2-{[2-({[(2R,3R,4R,5S,6R)-3-(ACETYLAMINO)-4,5-DIHYDROXY-6-(HYDROXYMETHYL)TETRAHYDRO-2H-PYRAN-2-YL]CARBAMOTHIOYL}AMINO)ETHYL](BIPHENYL-4-YLSULFONYL)AMINO}-3-METHYLBUTANOIC ACID (NON-PREFERRED NAME)
2CA-1Ligand/IonCALCIUM ION
3DIO2Ligand/Ion1,4-DIETHYLENE DIOXIDE
4DMS-1Ligand/IonDIMETHYL SULFOXIDE
5EDO-1Ligand/Ion1,2-ETHANEDIOL
6PGO1Ligand/IonS-1,2-PROPANEDIOL
7ZN-1Ligand/IonZINC ION
Biological Unit 3 (3, 3)
No.NameCountTypeFull Name
167F1Ligand/Ion(2S)-2-{[2-({[(2R,3R,4R,5S,6R)-3-(ACETYLAMINO)-4,5-DIHYDROXY-6-(HYDROXYMETHYL)TETRAHYDRO-2H-PYRAN-2-YL]CARBAMOTHIOYL}AMINO)ETHYL](BIPHENYL-4-YLSULFONYL)AMINO}-3-METHYLBUTANOIC ACID (NON-PREFERRED NAME)
2CA-1Ligand/IonCALCIUM ION
3DIO1Ligand/Ion1,4-DIETHYLENE DIOXIDE
4DMS-1Ligand/IonDIMETHYL SULFOXIDE
5EDO1Ligand/Ion1,2-ETHANEDIOL
6PGO-1Ligand/IonS-1,2-PROPANEDIOL
7ZN-1Ligand/IonZINC ION
Biological Unit 4 (2, 2)
No.NameCountTypeFull Name
167F1Ligand/Ion(2S)-2-{[2-({[(2R,3R,4R,5S,6R)-3-(ACETYLAMINO)-4,5-DIHYDROXY-6-(HYDROXYMETHYL)TETRAHYDRO-2H-PYRAN-2-YL]CARBAMOTHIOYL}AMINO)ETHYL](BIPHENYL-4-YLSULFONYL)AMINO}-3-METHYLBUTANOIC ACID (NON-PREFERRED NAME)
2CA-1Ligand/IonCALCIUM ION
3DIO-1Ligand/Ion1,4-DIETHYLENE DIOXIDE
4DMS1Ligand/IonDIMETHYL SULFOXIDE
5EDO-1Ligand/Ion1,2-ETHANEDIOL
6PGO-1Ligand/IonS-1,2-PROPANEDIOL
7ZN-1Ligand/IonZINC ION

(-) Sites  (32, 32)

Asymmetric Unit (32, 32)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREILE 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 , THR A:239 , TYR A:240 , ZN A:302 , HOH A:455 , GLU C:128binding site for residue 67F A 301
02AC2SOFTWAREHIS A:218 , HIS A:222 , HIS A:228 , 67F 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:452 , HOH A:462binding 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
07AC7SOFTWAREHIS A:172 , PHE A:185binding site for residue DMS A 307
08AC8SOFTWARELYS A:136 , THR A:205 , PHE A:213 , HOH A:439 , HOH A:472binding site for residue PGO A 308
09AC9SOFTWAREILE 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 , TYR B:240 , ZN B:302 , HOH B:450 , ASP D:231binding site for residue 67F B 301
10AD1SOFTWAREHIS B:218 , HIS B:222 , HIS B:228 , 67F B:301binding site for residue ZN B 302
11AD2SOFTWAREHIS B:168 , ASP B:170 , HIS B:183 , HIS B:196binding site for residue ZN B 303
12AD3SOFTWAREASP B:158 , GLY B:190 , GLY B:192 , ASP B:194 , HOH B:430 , HOH B:444binding site for residue CA B 304
13AD4SOFTWAREASP B:124 , GLU B:199 , GLU B:201 , HOH B:467 , HOH B:471binding site for residue CA B 305
14AD5SOFTWAREASP B:175 , GLY B:176 , GLY B:178 , ILE B:180 , ASP B:198 , GLU B:201binding site for residue CA B 306
15AD6SOFTWARELEU B:226 , SER B:229 , ASP B:253binding site for residue PGO B 307
16AD7SOFTWAREALA B:184 , PHE B:185binding site for residue DIO B 308
17AD8SOFTWAREALA B:133 , THR B:205 , HOH B:442binding site for residue DIO B 309
18AD9SOFTWAREARG A:135 , ASP C:175 , GLY 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 , HOH C:409 , HOH C:420binding site for residue 67F C 301
19AE1SOFTWAREHIS C:218 , HIS C:222 , HIS C:228 , 67F C:301binding site for residue ZN C 302
20AE2SOFTWAREHIS C:168 , ASP C:170 , HIS C:183 , HIS C:196binding site for residue ZN C 303
21AE3SOFTWAREASP C:158 , GLY C:190 , GLY C:192 , ASP C:194 , HOH C:410 , HOH C:437binding site for residue CA C 304
22AE4SOFTWAREASP C:124 , GLU C:199 , GLU C:201 , HOH C:468 , HOH C:469binding site for residue CA C 305
23AE5SOFTWAREASP C:175 , GLY C:176 , GLY C:178 , ILE C:180 , ASP C:198 , GLU C:201binding site for residue CA C 306
24AE6SOFTWARETHR C:205 , PHE C:213 , ILE C:245 , HOH C:407 , HOH C:435 , HOH C:470binding site for residue EDO C 307
25AE7SOFTWAREHIS C:183 , ALA C:184 , PHE C:185 , HOH C:431binding site for residue DIO C 308
26AE8SOFTWAREPRO B:232 , HOH B:423 , 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 , THR D:239 , TYR D:240 , ZN D:302 , DMS D:307 , HOH D:486binding site for residue 67F D 301
27AE9SOFTWAREHIS D:218 , HIS D:222 , HIS D:228 , 67F D:301binding site for residue ZN D 302
28AF1SOFTWAREHIS D:168 , ASP D:170 , HIS D:183 , HIS D:196binding site for residue ZN D 303
29AF2SOFTWAREASP D:158 , GLY D:190 , GLY D:192 , ASP D:194 , HOH D:415 , HOH D:440binding site for residue CA D 304
30AF3SOFTWAREASP D:124 , GLU D:199 , GLU D:201 , HOH D:429 , HOH D:450binding site for residue CA D 305
31AF4SOFTWAREASP D:175 , GLY D:176 , GLY D:178 , ILE D:180 , ASP D:198 , GLU D:201binding site for residue CA D 306
32AF5SOFTWAREHIS D:172 , ALA D:184 , 67F D:301binding site for residue DMS D 307

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5I3M)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5I3M)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5I3M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5I3M)

(-) Exons   (0, 0)

(no "Exon" information available for 5I3M)

(-) 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.....eehhhhhhhhhhhhh...................hhhhh..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5i3m 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..................hhhhh..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5i3m 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
                 5i3m 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: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..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5i3m D 107 PVWRKHYITYRINNYTPDMNREDVDYAIRKAFQVWSNVTPLKFSKINTGMADILVVFARGAHGDDHAFDGKGGILAHAFGPGSGIGGDAHFDEDEFWTTHSGGTNLFLTAVHQIGHSLGLGHSSDPKAVMFPTYKYVDINTFRLSADDIRGIQSLYG 263
                                   116       126       136       146       156       166       176       186       196       206       216       226       236       246       256
   Legend:   → Mismatch (orange background)
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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 5I3M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5I3M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5I3M)

(-) 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 5i2z 5i43 5i4o 5l79 5l7f 5lab

(-) Related Entries Specified in the PDB File

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