Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) 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
    ChainsA, B
    EC Number3.4.24.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPKA8H
    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

  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)
  - → 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 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)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    8OM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    AD1  [ RasMol ]  +environment [ RasMol ]
    AD2  [ RasMol ]  +environment [ RasMol ]
    AD3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Phe A:107 - Pro A:108   [ RasMol ]  
    Phe B:107 - Pro B:108   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5uwk
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  MMP13_HUMAN | P45452
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.4.24.-
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  MMP13_HUMAN | P45452
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 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 5uwl 5uwm 5uwn 830c

(-) Related Entries Specified in the PDB File

5uwl 5uwm 5uwn