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(-) Description

Title :  MATRIX METALLOPROTEINASE-13 COMPLEXED WITH SELECTIVE INHIBITOR COMPOUND (R)-17A
 
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 :  1.62
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (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
 
Molecule 2 - COLLAGENASE 3
    ChainsC, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPKA8H
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsPROTEOLYTIC FRAGMENT

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A C 
Biological Unit 2 (1x) B D

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 12)
No.NameCountTypeFull Name
18OA2Ligand/Ion(R)-N-(3-METHYL-1-(METHYLAMINO)-1-OXOBUTAN-2-YL)-5-(4-(((4-OXO-4,5,6,7-TETRAHYDRO-3H-CYCLOPENTA[D]PYRIMIDIN-2-YL)THIO)METHYL)PHENYL)FURAN-2-CARBOXAMIDE
2CA6Ligand/IonCALCIUM ION
3ZN4Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
18OA1Ligand/Ion(R)-N-(3-METHYL-1-(METHYLAMINO)-1-OXOBUTAN-2-YL)-5-(4-(((4-OXO-4,5,6,7-TETRAHYDRO-3H-CYCLOPENTA[D]PYRIMIDIN-2-YL)THIO)METHYL)PHENYL)FURAN-2-CARBOXAMIDE
2CA-1Ligand/IonCALCIUM ION
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
18OA1Ligand/Ion(R)-N-(3-METHYL-1-(METHYLAMINO)-1-OXOBUTAN-2-YL)-5-(4-(((4-OXO-4,5,6,7-TETRAHYDRO-3H-CYCLOPENTA[D]PYRIMIDIN-2-YL)THIO)METHYL)PHENYL)FURAN-2-CARBOXAMIDE
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 , ASN C:215binding 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:498 , HOH A:525binding site for residue CA A 304
05AC5SOFTWAREASP A:162 , ASN A:194 , GLY A:196 , ASP A:198 , HOH A:418 , HOH A:434binding site for residue CA A 305
06AC6SOFTWAREGLY A:183 , LEU A:184 , LEU A:185 , 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 , PRO A:255 , HOH A:474 , PHE B:241 , PRO B:242 , ILE B:243 , 8OA B:306 , ASN C:215binding site for residue 8OA A 306
07AC7SOFTWAREHIS B:222 , HIS B:226 , HIS B:232 , ASN D:215binding 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:492 , HOH B:496binding site for residue CA B 304
11AD2SOFTWAREASP B:162 , ASN B:194 , GLY B:196 , ASP B:198 , HOH B:418 , HOH B:431binding site for residue CA B 305
12AD3SOFTWARE8OA A:306 , LEU B:184 , LEU B:185 , LEU B:218 , HIS B:222 , GLU B:223 , GLY B:237 , LEU B:239 , PHE B:241 , PRO B:242 , ILE B:243 , TYR B:244 , THR B:245 , HOH B:454 , HOH B:465 , HOH C:305 , ASN D:215binding site for residue 8OA B 306

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5UWM)

(-) 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:155
                                                                                                                                                                                           
               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
                 5uwm A 111 LKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNFTRLHDGIADIMISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDDDETWTSSSKGYNLFLVAAHEFGHSLGLDHSKDPGALMFPIYTYTHFMLPDDDVQGIQSLYGP 268
                                   120       130       140       150       160       170       180       190       200       210       220       230       240      |253       263     
                                                                                                                                                                  247|                 
                                                                                                                                                                   251                 

Chain B from PDB  Type:PROTEIN  Length:154
                                                                                                                                                                                          
               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
                 5uwm B 111 LKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNFTRLHDGIADIMISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDDDETWTSSSKGYNLFLVAAHEFGHSLGLDHSKDPGALMFPIYTYFMLPDDDVQGIQSLYGPG 269
                                   120       130       140       150       160       170       180       190       200       210       220       230       240     ||255       265    
                                                                                                                                                                 246|                 
                                                                                                                                                                  252                 

Chain C from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..... Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 5uwm C 211 VTPLN 215

Chain D from PDB  Type:PROTEIN  Length:4
                                    
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 5uwm D 212 TPLN 215

   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 5UWM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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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 5uwn 830c

(-) Related Entries Specified in the PDB File

5uwk 5uwl 5uwn