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(-) Description

Title :  MATRIX METALLOPROTEINASE-13 COMPLEXED WITH SELECTIVE INHIBITOR COMPOUND 10D
 
Authors :  A. B. Taylor, X. Cao, P. J. Hart
Date :  21 Feb 17  (Deposition) - 12 Jul 17  (Release) - 12 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym. Unit :  A,B,C,D,E
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Biol. Unit 5:  E  (1x)
Keywords :  Metalloproteinase, Collagenase, Mmp-13, Hydrolase, Hydrolase- Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Y. Choi, R. Fuerst, A. M. Knapinska, A. B. Taylor, L. Smith, X. Cao, P. J. Hart, G. B. Fields, W. R. Roush
Structure-Based Design And Synthesis Of Potent And Selectiv Matrix Metalloproteinase 13 Inhibitors.
J. Med. Chem. 2017
PubMed-ID: 28653849  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.7B00514

(-) Compounds

Molecule 1 - COLLAGENASE 3
    ChainsA, B, C, D, E
    EC Number3.4.24.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPAK8H
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneMMP13
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCATALYTIC DOMAIN (UNP RESIDUES 104-274)
    SynonymMATRIX METALLOPROTEINASE-13,MMP-13

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit ABCDE
Biological Unit 1 (1x)A    
Biological Unit 2 (1x) B   
Biological Unit 3 (1x)  C  
Biological Unit 4 (1x)   D 
Biological Unit 5 (1x)    E

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 39)

Asymmetric Unit (4, 39)
No.NameCountTypeFull Name
18O75Ligand/IonN-(2-AMINOETHYL)-4'-(((4-OXO-4,5,6,7-TETRAHYDRO-3H-CYCLOPENTA[D]PYRIMIDIN-2-YL)THIO)METHYL)-[1,1'-BIPHENYL]-4-SULFONAMIDE
2CA10Ligand/IonCALCIUM ION
3SO414Ligand/IonSULFATE ION
4ZN10Ligand/IonZINC ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
18O71Ligand/IonN-(2-AMINOETHYL)-4'-(((4-OXO-4,5,6,7-TETRAHYDRO-3H-CYCLOPENTA[D]PYRIMIDIN-2-YL)THIO)METHYL)-[1,1'-BIPHENYL]-4-SULFONAMIDE
2CA-1Ligand/IonCALCIUM ION
3SO42Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
18O71Ligand/IonN-(2-AMINOETHYL)-4'-(((4-OXO-4,5,6,7-TETRAHYDRO-3H-CYCLOPENTA[D]PYRIMIDIN-2-YL)THIO)METHYL)-[1,1'-BIPHENYL]-4-SULFONAMIDE
2CA-1Ligand/IonCALCIUM ION
3SO42Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION
Biological Unit 3 (2, 3)
No.NameCountTypeFull Name
18O71Ligand/IonN-(2-AMINOETHYL)-4'-(((4-OXO-4,5,6,7-TETRAHYDRO-3H-CYCLOPENTA[D]PYRIMIDIN-2-YL)THIO)METHYL)-[1,1'-BIPHENYL]-4-SULFONAMIDE
2CA-1Ligand/IonCALCIUM ION
3SO42Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION
Biological Unit 4 (2, 6)
No.NameCountTypeFull Name
18O71Ligand/IonN-(2-AMINOETHYL)-4'-(((4-OXO-4,5,6,7-TETRAHYDRO-3H-CYCLOPENTA[D]PYRIMIDIN-2-YL)THIO)METHYL)-[1,1'-BIPHENYL]-4-SULFONAMIDE
2CA-1Ligand/IonCALCIUM ION
3SO45Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION
Biological Unit 5 (2, 4)
No.NameCountTypeFull Name
18O71Ligand/IonN-(2-AMINOETHYL)-4'-(((4-OXO-4,5,6,7-TETRAHYDRO-3H-CYCLOPENTA[D]PYRIMIDIN-2-YL)THIO)METHYL)-[1,1'-BIPHENYL]-4-SULFONAMIDE
2CA-1Ligand/IonCALCIUM ION
3SO43Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION

(-) Sites  (39, 39)

Asymmetric Unit (39, 39)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:222 , GLU A:223 , HIS A:226 , HIS A:232binding site for residue ZN A 301
02AC2SOFTWAREHIS A:172 , ASP A:174 , HIS A:187 , HIS A:200binding site for residue ZN A 302
03AC3SOFTWAREASP A:179 , GLY A:180 , SER A:182 , LEU A:184 , ASP A:202 , GLU A:205binding site for residue CA A 303
04AC4SOFTWAREASP A:162 , ASN A:194 , GLY A:196 , ASP A:198binding site for residue CA A 304
05AC5SOFTWARELEU A:184 , LEU A:185 , ALA A:186 , LEU A:218 , HIS A:222 , GLU A:223 , LEU A:239 , PHE A:241 , PRO A:242 , ILE A:243 , TYR A:244 , THR A:245 , THR A:247 , LYS A:249binding site for residue 8O7 A 305
06AC6SOFTWARELYS A:115 , MET A:116 , ASN A:117binding site for residue SO4 A 306
07AC7SOFTWARETYR A:120 , LYS A:139 , ARG A:155binding site for residue SO4 A 307
08AC8SOFTWAREHIS B:222 , HIS B:226 , HIS B:232binding site for residue ZN B 301
09AC9SOFTWAREHIS B:172 , ASP B:174 , HIS B:187 , HIS B:200binding site for residue ZN B 302
10AD1SOFTWAREASP B:179 , GLY B:180 , SER B:182 , LEU B:184 , ASP B:202 , GLU B:205binding site for residue CA B 303
11AD2SOFTWAREALA B:161 , ASP B:162 , ASN B:194 , GLY B:196 , ASP B:198binding site for residue CA B 304
12AD3SOFTWARELEU B:184 , LEU B:185 , ALA B:186 , LEU B:218 , HIS B:222 , GLU B:223 , GLY B:237 , ALA B:238 , LEU B:239 , PHE B:241 , PRO B:242 , ILE B:243 , TYR B:244 , THR B:245 , THR B:247 , PHE B:252binding site for residue 8O7 B 305
13AD4SOFTWARELYS B:115 , MET B:116 , ASN B:117binding site for residue SO4 B 306
14AD5SOFTWARETYR B:120 , LYS B:139 , ARG B:155binding site for residue SO4 B 307
15AD6SOFTWAREHIS C:222 , HIS C:226 , HIS C:232binding site for residue ZN C 301
16AD7SOFTWAREHIS C:172 , ASP C:174 , HIS C:187 , HIS C:200binding site for residue ZN C 302
17AD8SOFTWAREASP C:179 , GLY C:180 , SER C:182 , LEU C:184 , ASP C:202 , GLU C:205binding site for residue CA C 303
18AD9SOFTWAREASP C:162 , ASN C:194 , GLY C:196 , ASP C:198binding site for residue CA C 304
19AE1SOFTWAREGLY C:183 , LEU C:184 , LEU C:185 , ALA C:186 , LEU C:218 , VAL C:219 , ALA C:238 , LEU C:239 , PHE C:241 , PRO C:242 , ILE C:243 , TYR C:244 , THR C:245 , TYR C:246 , PHE C:252 , PRO C:255binding site for residue 8O7 C 305
20AE2SOFTWARETHR C:130 , HIS C:131 , THR E:130 , HIS E:131binding site for residue SO4 C 306
21AE3SOFTWAREGLU C:135 , LYS C:139 , ARG C:155binding site for residue SO4 C 307
22AE4SOFTWAREHIS D:222 , GLU D:223 , HIS D:226 , HIS D:232binding site for residue ZN D 301
23AE5SOFTWAREHIS D:172 , ASP D:174 , HIS D:187 , HIS D:200binding site for residue ZN D 302
24AE6SOFTWAREASP D:179 , GLY D:180 , SER D:182 , LEU D:184 , ASP D:202 , GLU D:205binding site for residue CA D 303
25AE7SOFTWAREASP D:162 , ASN D:194 , GLY D:196 , ASP D:198binding site for residue CA D 304
26AE8SOFTWARELEU D:184 , LEU D:185 , ALA D:186 , LEU D:218 , VAL D:219 , HIS D:222 , GLU D:223 , GLY D:237 , LEU D:239 , PHE D:241 , PRO D:242 , ILE D:243 , THR D:245 , THR D:247 , PHE D:252 , PRO D:255binding site for residue 8O7 D 305
27AE9SOFTWARELYS B:234 , LYS D:115 , MET D:116 , ASN D:117binding site for residue SO4 D 306
28AF1SOFTWARETHR A:130 , HIS A:131 , THR D:130 , HIS D:131binding site for residue SO4 D 307
29AF2SOFTWARETHR D:130 , SER D:132binding site for residue SO4 D 308
30AF3SOFTWARETYR D:120 , LYS D:139 , ARG D:155binding site for residue SO4 D 309
31AF4SOFTWARETHR D:208 , SER D:210 , LYS D:212binding site for residue SO4 D 310
32AF5SOFTWAREHIS E:222 , GLU E:223 , HIS E:226 , HIS E:232binding site for residue ZN E 301
33AF6SOFTWAREHIS E:172 , ASP E:174 , HIS E:187 , HIS E:200binding site for residue ZN E 302
34AF7SOFTWAREASP E:179 , GLY E:180 , SER E:182 , LEU E:184 , ASP E:202 , GLU E:205binding site for residue CA E 303
35AF8SOFTWAREASP E:162 , ASN E:194 , GLY E:196 , ASP E:198binding site for residue CA E 304
36AF9SOFTWARESER B:264 , PRO B:268 , MET E:103 , TYR E:104 , LEU E:184 , LEU E:185 , ALA E:186 , LEU E:218 , HIS E:222 , GLU E:223 , GLY E:237 , ALA E:238 , PHE E:241 , PRO E:242 , ILE E:243 , TYR E:244 , THR E:245 , THR E:247 , PRO E:255binding site for residue 8O7 E 305
37AG1SOFTWARELYS E:115 , MET E:116 , ASN E:117binding site for residue SO4 E 306
38AG2SOFTWARETYR E:120 , LYS E:139 , ARG E:155binding site for residue SO4 E 307
39AG3SOFTWARETHR E:208 , SER E:209 , SER E:210binding site for residue SO4 E 308

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Phe B:107 -Pro B:108
2Phe E:107 -Pro E:108

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5UWN)

(-) 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:161
                                                                                                                                                                                                 
               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
                 5uwn A 109 RTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNFTRLHDGIADIMISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDDDETWTSSSKGYNLFLVAAHEFGHSLGLDHSKDPGALMFPIYTYTGKSHFMLPDDDVQGIQSLYGPG 269
                                   118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268 

Chain B from PDB  Type:PROTEIN  Length:170
                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeee.......hhhhhhhhhhhhhhhhhh....eeeee......eeeeee.................eee..........eeee....ee.....eehhhhhhhhhhhhh..........................hhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5uwn B 104 YNVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNFTRLHDGIADIMISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDDDETWTSSSKGYNLFLVAAHEFGHSLGLDHSKDPGALMFPIYTYTGKSHFMLPDDDVQGIQSLYGPGDEDP 273
                                   113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273

Chain C from PDB  Type:PROTEIN  Length:166
                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeee.......hhhhhhhhhhhhhhhhhh....eeeee......eeeeee.................eee..........eeee....ee.....eehhhhhhhhhhhhh..........................hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5uwn C 104 YNVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNFTRLHDGIADIMISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDDDETWTSSSKGYNLFLVAAHEFGHSLGLDHSKDPGALMFPIYTYTGKSHFMLPDDDVQGIQSLYGPG 269
                                   113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263      

Chain D from PDB  Type:PROTEIN  Length:165
                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeee.......hhhhhhhhhhhhhhhhhh....eeeee......eeeeee.................eee..........eeee....ee.....eehhhhhhhhhhhhh..........................hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5uwn D 105 NVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNFTRLHDGIADIMISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDDDETWTSSSKGYNLFLVAAHEFGHSLGLDHSKDPGALMFPIYTYTGKSHFMLPDDDVQGIQSLYGPG 269
                                   114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264     

Chain E from PDB  Type:PROTEIN  Length:167
                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeee.......hhhhhhhhhhhhhhhhhh....eeeee......eeeeee.................eee..........eeee....ee.....eehhhhhhhhhhhhh..........................hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5uwn E 103 MYNVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNFTRLHDGIADIMISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDDDETWTSSSKGYNLFLVAAHEFGHSLGLDHSKDPGALMFPIYTYTGKSHFMLPDDDVQGIQSLYGPG 269
                                   112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       

   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 5UWN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5UWN)

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 Related Entries

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

UniProtKB/Swiss-Prot
        MMP13_HUMAN | P454521eub 1fls 1fm1 1pex 1uc1 1xuc 1xud 1xur 1you 1ztq 2d1n 2e2d 2ow9 2ozr 2pjt 2yig 3elm 3i7g 3i7i 3kec 3kej 3kek 3kry 3ljz 3o2x 3tvc 3wv1 3wv2 3wv3 3zxh 456c 4a7b 4fu4 4fvl 4g0d 4jp4 4jpa 4l19 5b5o 5b5p 5bot 5boy 5bpa 5uwk 5uwl 5uwm 830c

(-) Related Entries Specified in the PDB File

5uwk 5uwl 5uwm