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(-) Description

Title :  MATRIX METALLOPROTEINASE-13 COMPLEXED WITH SELECTIVE INHIBITOR COMPOUND Q1
 
Authors :  D. Minond, T. P. Spicer, J. Jiang, A. B. Taylor, P. J. Hart, W. R. Roush, G. P. S. Hodder
Date :  02 Jun 13  (Deposition) - 10 Dec 14  (Release) - 10 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.66
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (2x)
Keywords :  Metalloprotease, Hydrolase, Mmp-13, Collagenase, Exosite Inhibitor, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. P. Spicer, J. Jiang, A. B. Taylor, J. Y. Choi, P. J. Hart, W. R. Roush, G. B. Fields, P. S. Hodder, D. Minond
Characterization Of Selective Exosite-Binding Inhibitors Of Matrix Metalloproteinase 13 That Prevent Articular Cartilag Degradation In Vitro.
J. Med. Chem. V. 57 9598 2014
PubMed-ID: 25330343  |  Reference-DOI: 10.1021/JM501284E

(-) Compounds

Molecule 1 - COLLAGENASE 3
    Chains: A, B
    EC Number: 3.4.24.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKA8H
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: CATALYTIC DOMAIN (UNP RESIDUES 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 Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 20)

Asymmetric Unit (5, 20)
No.NameCountTypeFull Name
11UA3Ligand/Ion2-[(4-METHYLBENZYL)SULFANYL]-3,5,6,7-TETRAHYDRO-4H-CYCLOPENTA[D]PYRIMIDIN-4-ONE
2CA4Ligand/IonCALCIUM ION
3FMT5Ligand/IonFORMIC ACID
4GOL3Ligand/IonGLYCEROL
5ZN5Ligand/IonZINC ION
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
11UA2Ligand/Ion2-[(4-METHYLBENZYL)SULFANYL]-3,5,6,7-TETRAHYDRO-4H-CYCLOPENTA[D]PYRIMIDIN-4-ONE
2CA-1Ligand/IonCALCIUM ION
3FMT1Ligand/IonFORMIC ACID
4GOL1Ligand/IonGLYCEROL
5ZN-1Ligand/IonZINC ION
Biological Unit 2 (3, 7)
No.NameCountTypeFull Name
11UA1Ligand/Ion2-[(4-METHYLBENZYL)SULFANYL]-3,5,6,7-TETRAHYDRO-4H-CYCLOPENTA[D]PYRIMIDIN-4-ONE
2CA-1Ligand/IonCALCIUM ION
3FMT4Ligand/IonFORMIC ACID
4GOL2Ligand/IonGLYCEROL
5ZN-1Ligand/IonZINC ION
Biological Unit 3 (3, 22)
No.NameCountTypeFull Name
11UA6Ligand/Ion2-[(4-METHYLBENZYL)SULFANYL]-3,5,6,7-TETRAHYDRO-4H-CYCLOPENTA[D]PYRIMIDIN-4-ONE
2CA-1Ligand/IonCALCIUM ION
3FMT10Ligand/IonFORMIC ACID
4GOL6Ligand/IonGLYCEROL
5ZN-1Ligand/IonZINC ION

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:172 , ASP A:174 , HIS A:187 , HIS A:200BINDING SITE FOR RESIDUE ZN A 301
02AC2SOFTWAREHIS A:222 , HIS A:226 , HIS A:232 , FMT A:306BINDING SITE FOR RESIDUE ZN A 302
03AC3SOFTWAREHIS A:131 , SER A:250 , HIS A:251 , GOL A:309BINDING SITE FOR RESIDUE ZN 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:407 , HOH A:458BINDING SITE FOR RESIDUE CA A 305
06AC6SOFTWAREHIS A:222 , GLU A:223 , HIS A:226 , HIS A:232 , ZN A:302 , 1UA A:308BINDING SITE FOR RESIDUE FMT A 306
07AC7SOFTWARELEU A:218 , HIS A:222 , LEU A:239 , PHE A:241 , ILE A:243 , THR A:245 , THR A:247 , PHE A:252BINDING SITE FOR RESIDUE 1UA A 307
08AC8SOFTWARETYR A:176 , ALA A:188 , PHE A:189 , HIS A:226 , FMT A:306 , HOH A:494BINDING SITE FOR RESIDUE 1UA A 308
09AC9SOFTWAREHIS A:131 , GLU A:135 , ARG A:155 , SER A:250 , ZN A:303 , PRO B:127BINDING SITE FOR RESIDUE GOL A 309
10BC1SOFTWAREHIS B:172 , ASP B:174 , HIS B:187 , HIS B:200BINDING SITE FOR RESIDUE ZN B 301
11BC2SOFTWAREHIS B:222 , HIS B:226 , HIS B:232 , FMT B:305BINDING SITE FOR RESIDUE ZN B 302
12BC3SOFTWAREASP B:162 , ASN B:194 , GLY B:196 , ASP B:198 , HOH B:489 , HOH B:505BINDING SITE FOR RESIDUE CA B 303
13BC4SOFTWAREASP B:179 , GLY B:180 , SER B:182 , LEU B:184 , ASP B:202 , GLU B:205BINDING SITE FOR RESIDUE CA B 304
14BC5SOFTWAREHIS B:222 , GLU B:223 , HIS B:226 , HIS B:232 , ZN B:302 , HOH B:458BINDING SITE FOR RESIDUE FMT B 305
15BC6SOFTWARETHR A:130 , HIS A:131 , THR B:130 , HIS B:131 , HOH B:408BINDING SITE FOR RESIDUE FMT B 306
16BC7SOFTWARELYS B:234 , GLN B:263 , HOH B:442 , HOH B:464BINDING SITE FOR RESIDUE FMT B 307
17BC8SOFTWARELYS B:115 , MET B:116 , ASN B:117 , HOH B:460BINDING SITE FOR RESIDUE FMT B 308
18BC9SOFTWAREHIS B:222 , GLY B:237 , LEU B:239 , PHE B:241 , ILE B:243 , TYR B:244 , THR B:245 , PHE B:252BINDING SITE FOR RESIDUE 1UA B 309
19CC1SOFTWARETYR B:176 , ALA B:188 , HOH B:493 , HOH B:555BINDING SITE FOR RESIDUE GOL B 310
20CC2SOFTWAREARG B:155 , LEU B:156 , HIS B:157 , ASP B:158 , HOH B:413 , HOH B:498BINDING SITE FOR RESIDUE GOL B 311

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4L19)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4L19)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4L19)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4L19)

(-) Exons   (0, 0)

(no "Exon" information available for 4L19)

(-) 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:166
                                                                                                                                                                                                      
               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
                 4l19 A 104 YNVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNFTRLHDGIADIMISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDDDETWTSSSKGYNLFLVAAHEFGHSLGLDHSKDPGALMFPIYTYTGKSHFMLPDDDVQGIQSLYGPG 269
                                   113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263      


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.....eehhhhhhhhhhhhhh.........................hhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4l19 B 104 YNVFPRTLKWSKMNLTYRIVNYTPDMTHSEVEKAFKKAFKVWSDVTPLNFTRLHDGIADIMISFGIKEHGDFYPFDGPSGLLAHAFPPGPNYGGDAHFDDDETWTSSSKGYNLFLVAAHEFGHSLGLDHSKDPGALMFPIYTYTGKSHFMLPDDDVQGIQSLYGPGDEDP 273
                                   113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273
   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 4L19)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4L19)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4L19)

(-) Gene Ontology  (42, 42)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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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 5b5o 5b5p 5bot 5boy 5bpa 5uwk 5uwl 5uwm 5uwn 830c

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