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(-) Description

Title :  MATRIX METALLOPROTEINASE-13 COMPLEXED WITH SELECTIVE INHIBITOR COMPOUND (S)-10A
 
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 :  1.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (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
    Chains: A, B
    EC Number: 3.4.24.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PKA8H
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: MMP13
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: CATALYTIC DOMAIN (UNP RESIDUES 104-274)
    Synonym: MATRIX METALLOPROTEINASE-13,MMP-13

 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  (3, 12)

Asymmetric Unit (3, 12)
No.NameCountTypeFull Name
18OM2Ligand/Ion(S)-3-METHYL-2-(4'-(((4-OXO-4,5,6,7-TETRAHYDRO-3H-CYCLOPENTA[D]PYRIMIDIN-2-YL)THIO)METHYL)-[1,1'-BIPHENYL]-4-YLSULFONAMIDO)BUTANOIC ACID
2CA6Ligand/IonCALCIUM ION
3ZN4Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
18OM1Ligand/Ion(S)-3-METHYL-2-(4'-(((4-OXO-4,5,6,7-TETRAHYDRO-3H-CYCLOPENTA[D]PYRIMIDIN-2-YL)THIO)METHYL)-[1,1'-BIPHENYL]-4-YLSULFONAMIDO)BUTANOIC ACID
2CA-1Ligand/IonCALCIUM ION
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
18OM1Ligand/Ion(S)-3-METHYL-2-(4'-(((4-OXO-4,5,6,7-TETRAHYDRO-3H-CYCLOPENTA[D]PYRIMIDIN-2-YL)THIO)METHYL)-[1,1'-BIPHENYL]-4-YLSULFONAMIDO)BUTANOIC ACID
2CA-1Ligand/IonCALCIUM ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:222 , HIS A:226 , HIS A:232 , 8OM A:306binding 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:128 , ASP A:203 , GLU A:205 , HOH A:427 , HOH A:512binding site for residue CA A 304
05AC5SOFTWAREASP A:162 , ASN A:194 , GLY A:196 , ASP A:198 , HOH A:416 , HOH A:466binding site for residue CA A 305
06AC6SOFTWARELEU A:184 , LEU A:185 , ALA A:186 , LEU A:218 , HIS A:222 , GLU A:223 , HIS A:226 , HIS A:232 , GLY A:237 , LEU A:239 , PHE A:241 , PRO A:242 , ILE A:243 , TYR A:244 , THR A:245 , THR A:247 , PHE A:252 , PRO A:255 , ZN A:301 , HOH A:460 , HOH A:493 , HOH A:517binding site for residue 8OM A 306
07AC7SOFTWAREHIS B:222 , HIS B:226 , HIS B:232 , 8OM B:306binding site for residue ZN B 301
08AC8SOFTWAREHIS B:172 , ASP B:174 , HIS B:187 , HIS B:200binding site for residue ZN B 302
09AC9SOFTWAREASP B:179 , GLY B:180 , SER B:182 , LEU B:184 , ASP B:202 , GLU B:205binding site for residue CA B 303
10AD1SOFTWAREASP B:128 , ASP B:203 , GLU B:205 , HOH B:424 , HOH B:523binding site for residue CA B 304
11AD2SOFTWAREASP B:162 , ASN B:194 , GLY B:196 , ASP B:198 , HOH B:415 , HOH B:458binding site for residue CA B 305
12AD3SOFTWAREPHE A:107 , LEU B:184 , LEU B:185 , ALA B:186 , LEU B:218 , HIS B:222 , GLU B:223 , HIS B:226 , HIS B:232 , LEU B:239 , PHE B:241 , PRO B:242 , ILE B:243 , TYR B:244 , THR B:245 , THR B:247 , ZN B:301 , HOH B:450 , HOH B:497binding site for residue 8OM B 306

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5UWK)

(-) 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:160
                                                                                                                                                                                                
               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
                 5uwk A 107 FPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNFTRLHDGIADIMISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDDDETWTSSSKGYNLFLVAAHEFGHSLGLDHSKDPGALMFPIYTYTGFMLPDDDVQGIQSLYGPG 269
                                   116       126       136       146       156       166       176       186       196       206       216       226       236       246 ||    259       269
                                                                                                                                                                       248|                 
                                                                                                                                                                        252                 


Chain B 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
                 5uwk B 107 FPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNFTRLHDGIADIMISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDDDETWTSSSKGYNLFLVAAHEFGHSLGLDHSKDPGALMFPIYTYTGHFMLPDDDVQGIQSLYGPG 269
                                   116       126       136       146       156       166       176       186       196       206       216       226       236       246 ||    258       268 
                                                                                                                                                                       248|                  
                                                                                                                                                                        251
   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 5UWK)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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    Phe A:107 - Pro A:108   [ RasMol ]  
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        MMP13_HUMAN | P45452: 1eub 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 5uwl 5uwm 5uwn 830c

(-) Related Entries Specified in the PDB File

5uwl 5uwm 5uwn