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

(-) Description

Title :  X-RAY CO-STRUCTURE OF MMP-13 WITH 4-[({5-[2-(ETHOXYCARBONYL)-1H-INDOL-5-YL]-1-METHYL-1H-PYRAZOL-3-YL}FORMAMIDO)METHYL]BENZOATE
 
Authors :  N. A. Farrow, S. M. Margarit
Date :  27 May 15  (Deposition) - 17 Jun 15  (Release) - 20 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.79
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ridgefield, Protease, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. J. Taylor, A. Abeywardane, S. Liang, I. Muegge, A. K. Padyana, Z. Xiong, M. Hill-Drzewi, B. Farmer, X. Li, B. Collins, J. X. Li, A. Heim-Riether, J. Proudfoot, Q. Zhang, D. Goldberg, L. Zuvela-Jelaska, H. Zaher, J. Li, N. A. Farrow
Fragment-Based Discovery Of Indole Inhibitors Of Matrix Metalloproteinase-13.
J. Med. Chem. V. 54 8174 2011
PubMed-ID: 22017539  |  Reference-DOI: 10.1021/JM201129M

(-) Compounds

Molecule 1 - COLLAGENASE 3
    Chains: A, B
    EC Number: 3.4.24.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: UNP RESIDUES 104-274
    Fragment (source): 104-274
    Gene: MMP13
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: MATRIX METALLOPROTEINASE-13,MMP-13

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric/Biological Unit (3, 12)
No.NameCountTypeFull Name
14UF2Ligand/Ion4-{[({5-[2-(ETHOXYCARBONYL)-1H-INDOL-5-YL]-1-METHYL-1H-PYRAZOL-3-YL}CARBONYL)AMINO]METHYL}BENZOIC ACID
2CA6Ligand/IonCALCIUM ION
3ZN4Ligand/IonZINC ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:222 , 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:128 , ASP A:203 , GLU A:205 , HOH B:488binding site for residue CA A 303
04AC4SOFTWAREASP A:179 , GLY A:180 , SER A:182 , LEU A:184 , ASP A:202 , GLU A:205binding site for residue CA A 304
05AC5SOFTWAREASP A:162 , ASN A:194 , GLY A:196 , ASP A:198 , HOH A:416binding site for residue CA A 305
06AC6SOFTWARELYS A:140 , LEU A:185 , ASN A:215 , PHE A:217 , LEU A:218 , HIS A:222 , GLU A:223 , ALA A:238 , LEU A:239 , PHE A:241 , PRO A:242 , ILE A:243 , THR A:245 , TYR A:246 , THR A:247 , LYS A:249 , PHE A:252 , HOH A:410 , HOH A:429 , HOH A:474binding site for residue 4UF A 306
07AC7SOFTWAREHIS B:222 , HIS B:226 , HIS B:232binding site for residue ZN B 301
08AC8SOFTWAREHIS B:172 , ASP B:174 , HIS B:187 , HIS B:200binding site for residue ZN B 302
09AC9SOFTWAREHOH A:501 , ASP B:128 , ASP B:203 , GLU B:205binding site for residue CA B 303
10AD1SOFTWAREASP B:179 , GLY B:180 , SER B:182 , LEU B:184 , ASP B:202 , GLU B:205binding site for residue CA B 304
11AD2SOFTWAREASP B:162 , ASN B:194 , GLY B:196 , ASP B:198binding site for residue CA B 305
12AD3SOFTWARELYS B:140 , ASN B:215 , PHE B:217 , LEU B:218 , VAL B:219 , HIS B:222 , GLU B:223 , ALA B:238 , LEU B:239 , PHE B:241 , ILE B:243 , THR B:245 , TYR B:246 , THR B:247 , LYS B:249 , SER B:250 , HIS B:251 , PHE B:252 , HOH B:440 , HOH B:446binding site for residue 4UF B 306

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5BPA)

(-) Sequences/Alignments

Asymmetric/Biological 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:169
                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeee.......hhhhhhhhhhhhhhhhhh....eeeee......eeeeee.................eee..........eeee....ee.....eehhhhhhhhhhhhhh.........................hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bpa A 104 YNVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNFTRLHDGIADIMISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDDDETWTSSSKGYNLFLVAAHEFGHSLGLDHSKDPGALMFPIYTYTGKSHFMLPDDDVQGIQSLYGPGDED 272
                                   113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263         


Chain B from PDB  Type:PROTEIN  Length:166
                                                                                                                                                                                                      
               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
                 5bpa B 104 YNVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNFTRLHDGIADIMISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDDDETWTSSSKGYNLFLVAAHEFGHSLGLDHSKDPGALMFPIYTYTGKSHFMLPDDDVQGIQSLYGPG 269
                                   113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263
   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 5BPA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (42, 42)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    4UF  [ 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
(no "Cis Peptide Bonds" information available for 5bpa)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5bpa
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  MMP13_HUMAN | P45452
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.4.24.-
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  MMP13_HUMAN | P45452
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        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 5uwk 5uwl 5uwm 5uwn 830c

(-) Related Entries Specified in the PDB File

5boy