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(-) Description

Title :  CRYSTAL STRUCTURE OF MUTANT MMP-9 CATALYTIC DOMAIN IN COMPLEX WITH A TWIN INHIBITOR.
 
Authors :  E. A. Stura, L. Vera, E. Cassar-Lajeunesse, E. Nuti, M. P. Catalani, V. D A. Rossello
Date :  11 Sep 12  (Deposition) - 24 Apr 13  (Release) - 12 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.59
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase/Twin Inhibitor, Zincin-Like, Gelatinase, Collagenase (Catalytic Domain), Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Antoni, L. Vera, L. Devel, M. P. Catalani, B. Czarny, E. Cassar-Lajeunesse, E. Nuti, A. Rossello, V. Dive, E. A. Stura
Crystallization Of Bi-Functional Ligand Protein Complexes.
J. Struct. Biol. V. 182 246 2013
PubMed-ID: 23567804  |  Reference-DOI: 10.1016/J.JSB.2013.03.015

(-) Compounds

Molecule 1 - MATRIX METALLOPROTEINASE-9
    Chains: A, B
    EC Number: 3.4.24.35
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-14B
    Expression System Strain: BL21 (DE3 STAR)
    Expression System Taxid: 469008
    Expression System Vector Type: PT7 PROMOTER
    Fragment: UNP RESIDUES 110-214
    Gene: CLG4B, MMP9
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: MMP-9, 92 KDA GELATINASE, 92 KDA TYPE IV COLLAGENASE, GELATINASE B, GELB, 67 KDA MATRIX METALLOPROTEINASE-9, 82 KDA MATRIX METALLOPROTEINASE-9

 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, 13)

Asymmetric Unit (3, 13)
No.NameCountTypeFull Name
10XX2Ligand/IonN-(4-{[(3R)-3-[(BIPHENYL-4-YLSULFONYL)(PROPAN-2-YLOXY)AMINO]-4-(HYDROXYAMINO)-4-OXOBUTYL]AMINO}-4-OXOBUTYL)-N'-(4-{[(3S)-3-[(BIPHENYL-4-YLSULFONYL)(PROPAN-2-YLOXY)AMINO]-4-(HYDROXYAMINO)-4-OXOBUTYL]AMINO}-4-OXOBUTYL)BENZENE-1,3-DICARBOXAMIDE
2CA7Ligand/IonCALCIUM ION
3ZN4Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
10XX1Ligand/IonN-(4-{[(3R)-3-[(BIPHENYL-4-YLSULFONYL)(PROPAN-2-YLOXY)AMINO]-4-(HYDROXYAMINO)-4-OXOBUTYL]AMINO}-4-OXOBUTYL)-N'-(4-{[(3S)-3-[(BIPHENYL-4-YLSULFONYL)(PROPAN-2-YLOXY)AMINO]-4-(HYDROXYAMINO)-4-OXOBUTYL]AMINO}-4-OXOBUTYL)BENZENE-1,3-DICARBOXAMIDE
2CA-1Ligand/IonCALCIUM ION
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
10XX1Ligand/IonN-(4-{[(3R)-3-[(BIPHENYL-4-YLSULFONYL)(PROPAN-2-YLOXY)AMINO]-4-(HYDROXYAMINO)-4-OXOBUTYL]AMINO}-4-OXOBUTYL)-N'-(4-{[(3S)-3-[(BIPHENYL-4-YLSULFONYL)(PROPAN-2-YLOXY)AMINO]-4-(HYDROXYAMINO)-4-OXOBUTYL]AMINO}-4-OXOBUTYL)BENZENE-1,3-DICARBOXAMIDE
2CA-1Ligand/IonCALCIUM ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:226 , HIS A:230 , HIS A:236 , 0XX A:307BINDING SITE FOR RESIDUE ZN A 301
02AC2SOFTWAREHIS A:175 , ASP A:177 , HIS A:190 , HIS A:203BINDING SITE FOR RESIDUE ZN A 302
03AC3SOFTWAREASP A:165 , GLY A:197 , GLN A:199 , ASP A:201 , HOH A:477 , HOH A:481BINDING SITE FOR RESIDUE CA A 303
04AC4SOFTWAREASP A:131 , ASP A:206 , GLU A:208 , HOH A:421BINDING SITE FOR RESIDUE CA A 304
05AC5SOFTWAREASP A:182 , GLY A:183 , ASP A:185 , LEU A:187 , ASP A:205 , GLU A:208BINDING SITE FOR RESIDUE CA A 305
06AC6SOFTWARESER A:149 , THR A:152 , LEU A:154 , HOH A:496BINDING SITE FOR RESIDUE CA A 306
07AC7SOFTWARETYR A:179 , PRO A:180 , PHE A:181 , ASP A:182 , LEU A:187 , LEU A:188 , ALA A:189 , HIS A:190 , ALA A:191 , PHE A:192 , PRO A:193 , LEU A:222 , HIS A:226 , GLN A:227 , HIS A:230 , HIS A:236 , LEU A:243 , TYR A:245 , PRO A:246 , MET A:247 , TYR A:248 , ZN A:301 , HOH A:449 , HOH A:526 , PRO B:240 , GLU B:241 , TYR B:245 , PRO B:246 , ARG B:249BINDING SITE FOR RESIDUE 0XX A 307
08AC8SOFTWAREHIS B:226 , HIS B:230 , HIS B:236 , 0XX B:306BINDING SITE FOR RESIDUE ZN B 301
09AC9SOFTWAREHIS B:175 , ASP B:177 , HIS B:190 , HIS B:203BINDING SITE FOR RESIDUE ZN B 302
10BC1SOFTWAREASP B:165 , GLY B:197 , GLN B:199 , ASP B:201 , HOH B:487 , HOH B:489BINDING SITE FOR RESIDUE CA B 303
11BC2SOFTWAREASP B:131 , ASP B:206 , GLU B:208 , HOH B:517 , HOH B:518BINDING SITE FOR RESIDUE CA B 304
12BC3SOFTWAREASP B:182 , GLY B:183 , ASP B:185 , LEU B:187 , ASP B:205 , GLU B:208BINDING SITE FOR RESIDUE CA B 305
13BC4SOFTWARETYR A:245 , PRO A:246 , HOH A:523 , GLY B:112 , LEU B:187 , LEU B:188 , ALA B:189 , HIS B:190 , ALA B:191 , PRO B:193 , LEU B:222 , HIS B:226 , GLN B:227 , HIS B:230 , GLY B:233 , LEU B:234 , ASP B:235 , HIS B:236 , LEU B:243 , TYR B:245 , PRO B:246 , MET B:247 , TYR B:248 , HIS B:266 , ZN B:301 , HOH B:432 , HOH B:433 , HOH B:446 , HOH B:483 , HOH B:526BINDING SITE FOR RESIDUE 0XX B 306

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4H1Q)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4H1Q)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4H1Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4H1Q)

(-) Exons   (0, 0)

(no "Exon" information available for 4H1Q)

(-) 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 d4h1qa_ A: Gelatinase B (MMP-9)                                                                                                                                  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
                 4h1q A 110 FEGDLKWHHHNITYWIQNYSEDLPRAVIDDAFARAFALWSAVTPLTFTRVYSRDADIVIQFGVAEHGDGYPFDGKDGLLAHAFPPGPGIQGDAHFDDDELWSLGKGQGYSLFLVAAHQFGHALGLDHSSVPEALMYPMYRFTEGPPLHKDDVNGIRHLYG 269
                                   119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269


Chain B from PDB  Type:PROTEIN  Length:160
                                                                                                                                                                                                
               SCOP domains d4h1qb_ B: Gelatinase B (MMP-9)                                                                                                                                  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
                 4h1q B 110 FEGDLKWHHHNITYWIQNYSEDLPRAVIDDAFARAFALWSAVTPLTFTRVYSRDADIVIQFGVAEHGDGYPFDGKDGLLAHAFPPGPGIQGDAHFDDDELWSLGKGQGYSLFLVAAHQFGHALGLDHSSVPEALMYPMYRFTEGPPLHKDDVNGIRHLYG 269
                                   119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269
   Legend:   → Mismatch (orange background)
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  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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4H1Q)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4H1Q)

(-) Gene Ontology  (38, 38)

Asymmetric Unit(hide GO term definitions)

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UniProtKB/Swiss-Prot
        MMP9_HUMAN | P14780: 1gkc 1gkd 1itv 1l6j 1lkg 2ovx 2ovz 2ow0 2ow1 2ow2 4h2e 4h3x 4h82 4hma 4jij 4jqg 4wzv 4xct 5cuh 5i12 5th6 5th9

(-) Related Entries Specified in the PDB File

2ow1 MMP-9 ACTIVE SITE MUTANT WITH TRIFLUOROMETHYL HYDROXAMATE INHIBITOR
4h2e
4h30
4h3x