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(-) Description

Title :  STRUCTURE DETERMINATION OF A POTENT, SELECTIVE ANTIBODY INHIBITOR OF HUMAN MMP9 (APO MMP9)
 
Authors :  T. C. Appleby, A. E. Greenstein, H. J. Kwon
Date :  29 Sep 16  (Deposition) - 01 Mar 17  (Release) - 03 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Metalloproteinase-9 Antibody Inhibitor, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. C. Appleby, A. E. Greenstein, M. Hung, A. Liclican, M. Velasquez, A. G. Villasenor, R. Wang, M. H. Wong, X. Liu, G. A. Papalia, B. E. Schultz, R. Sakowicz, V. Smith, H. J. Kwon
Biochemical Characterization And Structure Determination Of A Potent, Selective Antibody Inhibitor Of Human Mmp9.
J. Biol. Chem. V. 292 6810 2017
PubMed-ID: 28235803  |  Reference-DOI: 10.1074/JBC.M116.760579

(-) Compounds

Molecule 1 - MATRIX METALLOPROTEINASE-9,MATRIX METALLOPROTEINASE-9
    Chains: A, B, C, D
    EC Number: 3.4.24.35, 3.4.24.35
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: MMP9, CLG4B
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: MMP-9,92 KDA GELATINASE,92 KDA TYPE IV COLLAGENASE, GELATINASE B,GELB,MMP-9,92 KDA GELATINASE,92 KDA TYPE IV COLLAGENASE, GELATINASE B,GELB

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 20)

Asymmetric Unit (2, 20)
No.NameCountTypeFull Name
1CA12Ligand/IonCALCIUM ION
2ZN8Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2ZN-1Ligand/IonZINC ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2ZN-1Ligand/IonZINC ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2ZN-1Ligand/IonZINC ION

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:99 , HIS A:401 , HIS A:405 , HIS A:411binding site for residue ZN A 501
02AC2SOFTWAREHIS A:175 , ASP A:177 , HIS A:190 , HIS A:203binding site for residue ZN A 502
03AC3SOFTWAREASP A:165 , GLY A:197 , GLN A:199 , ASP A:201 , HOH A:610 , HOH A:629binding site for residue CA A 503
04AC4SOFTWAREASP A:182 , GLY A:183 , ASP A:185 , LEU A:187 , ASP A:205 , GLU A:208binding site for residue CA A 504
05AC5SOFTWAREASP A:131 , ASP A:206 , GLU A:208 , HOH A:648binding site for residue CA A 505
06AC6SOFTWARECYS B:99 , HIS B:401 , HIS B:405 , HIS B:411binding site for residue ZN B 501
07AC7SOFTWAREHIS B:175 , ASP B:177 , HIS B:190 , HIS B:203binding site for residue ZN B 502
08AC8SOFTWAREASP B:165 , GLY B:197 , GLN B:199 , ASP B:201 , HOH B:613 , HOH B:642binding site for residue CA B 503
09AC9SOFTWAREASP B:182 , GLY B:183 , ASP B:185 , LEU B:187 , ASP B:205 , GLU B:208binding site for residue CA B 504
10AD1SOFTWAREASP B:131 , ASP B:206 , GLU B:208binding site for residue CA B 505
11AD2SOFTWARECYS C:99 , HIS C:401 , HIS C:405 , HIS C:411binding site for residue ZN C 501
12AD3SOFTWAREHIS C:175 , ASP C:177 , HIS C:190 , HIS C:203binding site for residue ZN C 502
13AD4SOFTWAREASP C:165 , GLY C:197 , GLN C:199 , ASP C:201 , HOH C:632 , HOH C:656binding site for residue CA C 503
14AD5SOFTWAREASP C:182 , GLY C:183 , ASP C:185 , LEU C:187 , ASP C:205 , GLU C:208binding site for residue CA C 504
15AD6SOFTWAREASP C:131 , ASP C:206 , GLU C:208 , HOH C:617 , HOH C:783binding site for residue CA C 505
16AD7SOFTWARECYS D:99 , HIS D:401 , HIS D:405 , HIS D:411binding site for residue ZN D 501
17AD8SOFTWAREHIS D:175 , ASP D:177 , HIS D:190 , HIS D:203binding site for residue ZN D 502
18AD9SOFTWAREASP D:165 , GLY D:197 , GLN D:199 , ASP D:201 , HOH D:640 , HOH D:653binding site for residue CA D 503
19AE1SOFTWAREASP D:182 , GLY D:183 , ASP D:185 , LEU D:187 , ASP D:205 , GLU D:208binding site for residue CA D 504
20AE2SOFTWAREASP D:131 , ASP D:206 , GLU D:208 , HOH D:635binding site for residue CA D 505

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5TH6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5TH6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5TH6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5TH6)

(-) Exons   (0, 0)

(no "Exon" information available for 5TH6)

(-) 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:220
                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.......hhhhhhhhh........................eeeeee.......hhhhhhhhhhhhhhhhhhh...eeeee......eeeeee.................eee..........eeee....ee......eehhhhhhhhhhhhhh.......................hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5th6 A  41 DRQLAEEYLYRYGYTRVALGPALLLLQKQLSLPETGELDSATLKAMRTPRCGVPDLGRFQTFEGDLKWHHHNITYWIQNYSEDLPRAVIDDAFARAFALWSAVTPLTFTRVYSRDADIVIQFGVAEHGDGYPFDGKDGLLAHAFPPGPGIQGDAHFDDDELWSLGKGQGYSLFLVAAHEFGHALGLDHSSVPEALMYPMYRFTEGPPLHKDDVNGIRHLY 443
                                    50       |68        78        88        98       108       118       128       138       148       158       168       178       188       198       208      |393       403       413       423       433       443
                                            58|                                                                                                                                                 215|                                                    
                                             67                                                                                                                                                  391                                                    


Chain B from PDB  Type:PROTEIN  Length:211
                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh.hhhhhhhhhhh.........hhhhhh.......................eeeeee.......hhhhhhhhhhhhhhhhhhhh..eeeee......eeeeee.................eee..........eeee....ee.eehhhhhhhhhhhhh........................hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5th6 B  42 RQLAEEYLYRYGYTRVAGPALLLLQKQLSLPETGELDTLKAMRTPRCGVPDLGRFQTFEGDLKWHHHNITYWIQNYSEDLPRAVIDDAFARAFALWSAVTPLTFTRVYSRDADIVIQFGVAEHGDGYPFDGKDGLLAHAFPPGPGIQGDAHFDDDELWSGYSLFLVAAHEFGHALGLDHSSVPEALMYPMYRFTEGPPLHKDDVNGIRHLY 443
                                    51      ||70        80      ||92       102       112       122       132       142       152       162       172       182       192       202       392       402       412       422       432       442 
                                           58|                 87|                                                                                                                      211|                                                   
                                            68                  90                                                                                                                       392                                                   


Chain C from PDB  Type:PROTEIN  Length:221
                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.......hhhhhhhhh........................eeeeee.......hhhhhhhhhhhhhhhhhhhh..eeee.......eeeeee.................eee..........eeee....ee......eehhhhhhhhhhhhh........................hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5th6 C  40 TDRQLAEEYLYRYGYTRVALGPALLLLQKQLSLPETGELDSATLKAMRTPRCGVPDLGRFQTFEGDLKWHHHNITYWIQNYSEDLPRAVIDDAFARAFALWSAVTPLTFTRVYSRDADIVIQFGVAEHGDGYPFDGKDGLLAHAFPPGPGIQGDAHFDDDELWSLGKGQGYSLFLVAAHEFGHALGLDHSSVPEALMYPMYRFTEGPPLHKDDVNGIRHLY 443
                                    49        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       392       402       412       422       432       442 
                                             58|                                                                                                                                                 215|                                                    
                                              67                                                                                                                                                  391                                                    


Chain D from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.......hhhhhhhhh........................eeeeee.......hhhhhhhhhhhhhhhhhhh...eeee.......eeeeee.................eee..........eeee....ee..eehhhhhhhhhhhhh........................hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5th6 D  40 TDRQLAEEYLYRYGYTRVALGPALLLLQKQLSLPETGELDSATLKAMRTPRCGVPDLGRFQTFEGDLKWHHHNITYWIQNYSEDLPRAVIDDAFARAFALWSAVTPLTFTRVYSRDADIVIQFGVAEHGDGYPFDGKDGLLAHAFPPGPGIQGDAHFDDDELWSLGYSLFLVAAHEFGHALGLDHSSVPEALMYPMYRFTEGPPLHKDDVNGIRHLY 443
                                    49        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207    || 396       406       416       426       436       
                                             58|                                                                                                                                              212|                                                   
                                              67                                                                                                                                               392
   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 5TH6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5TH6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5TH6)

(-) Gene Ontology  (38, 38)

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  5th6
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  MMP9_HUMAN | P14780
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  3.4.24.35
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 Related Entries

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

UniProtKB/Swiss-Prot
        MMP9_HUMAN | P14780: 1gkc 1gkd 1itv 1l6j 1lkg 2ovx 2ovz 2ow0 2ow1 2ow2 4h1q 4h2e 4h3x 4h82 4hma 4jij 4jqg 4wzv 4xct 5cuh 5i12 5th9

(-) Related Entries Specified in the PDB File

5th9