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(-) Description

Title :  CRYSTAL STRUCTURE OF AN INACTIVE MUTANT OF MMP-9 CATALYTIC DOMAIN IN COMPLEX WITH A FLUOROGENIC SYNTHETIC PEPTIDIC SUBSTRATE WITH A FLUORINE ATOM.
 
Authors :  E. A. Stura, L. Vera, E. Cassar-Lajeunesse, I. Tranchant, M. Amoura, V.
Date :  20 Mar 13  (Deposition) - 12 Mar 14  (Release) - 16 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B,P,Q
Biol. Unit 1:  A,P  (1x)
Biol. Unit 2:  B,Q  (1x)
Biol. Unit 3:  A,B,P,Q  (1x)
Keywords :  Halogen-Water-Hydrogen Bridge, Zincin-Like, Gelatinase, Collagenase, Catalytic Domain, Hydrolase-Substrate Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Tranchant, L. Vera, B. Czarny, M. Amoura, E. Cassar, F. Beau, E. A. Stura, V. Dive
Halogen Bonding Controls Selectivity Of Fret Substrate Probes For Mmp-9.
Chem. Biol. V. 21 408 2014
PubMed-ID: 24583051  |  Reference-DOI: 10.1016/J.CHEMBIOL.2014.01.008

(-) Compounds

Molecule 1 - FLUOROGENIC PEPTIDIC SUBSTRATE (8MC)PLG(PFF)(DNW)AR(NH2)
    Chains: P, Q
    Engineered: YES
    Other Details: FLUOROGENIC SYNTHETIC L-PEPTIDE SUBSTRATE WITH LOWER CATALYTIC EFFICIENCY WITH MMP-9 THAN THE IODINE CONTAINING SUBSTRATE PDB CODE 4JIJ.
    Synthetic: YES
 
Molecule 2 - 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: 562
    Expression System Vector Type: PT7 PROMOTER
    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

  1234
Asymmetric Unit : ABPQ
Biological Unit 1 (1x): A P 
Biological Unit 2 (1x):  B Q
Biological Unit 3 (1x): ABPQ

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (12, 33)

Asymmetric Unit (12, 33)
No.NameCountTypeFull Name
18MC2Mod. Amino Acid(7-METHOXY-2-OXO-2H-CHROMEN-4-YL)ACETIC ACID
2AZI2Ligand/IonAZIDE ION
3CA3Ligand/IonCALCIUM ION
4DNW2Mod. Amino Acid3-[(2,4-DINITROPHENYL)AMINO]-L-ALANINE
5EDO7Ligand/Ion1,2-ETHANEDIOL
6GOL1Ligand/IonGLYCEROL
7NA3Ligand/IonSODIUM ION
8NH22Mod. Amino AcidAMINO GROUP
9PFF2Mod. Amino Acid4-FLUORO-L-PHENYLALANINE
10PGO2Ligand/IonS-1,2-PROPANEDIOL
11SR3Ligand/IonSTRONTIUM ION
12ZN4Ligand/IonZINC ION
Biological Unit 1 (8, 12)
No.NameCountTypeFull Name
18MC1Mod. Amino Acid(7-METHOXY-2-OXO-2H-CHROMEN-4-YL)ACETIC ACID
2AZI1Ligand/IonAZIDE ION
3CA-1Ligand/IonCALCIUM ION
4DNW1Mod. Amino Acid3-[(2,4-DINITROPHENYL)AMINO]-L-ALANINE
5EDO5Ligand/Ion1,2-ETHANEDIOL
6GOL1Ligand/IonGLYCEROL
7NA-1Ligand/IonSODIUM ION
8NH21Mod. Amino AcidAMINO GROUP
9PFF1Mod. Amino Acid4-FLUORO-L-PHENYLALANINE
10PGO1Ligand/IonS-1,2-PROPANEDIOL
11SR-1Ligand/IonSTRONTIUM ION
12ZN-1Ligand/IonZINC ION
Biological Unit 2 (7, 8)
No.NameCountTypeFull Name
18MC1Mod. Amino Acid(7-METHOXY-2-OXO-2H-CHROMEN-4-YL)ACETIC ACID
2AZI1Ligand/IonAZIDE ION
3CA-1Ligand/IonCALCIUM ION
4DNW1Mod. Amino Acid3-[(2,4-DINITROPHENYL)AMINO]-L-ALANINE
5EDO2Ligand/Ion1,2-ETHANEDIOL
6GOL-1Ligand/IonGLYCEROL
7NA-1Ligand/IonSODIUM ION
8NH21Mod. Amino AcidAMINO GROUP
9PFF1Mod. Amino Acid4-FLUORO-L-PHENYLALANINE
10PGO1Ligand/IonS-1,2-PROPANEDIOL
11SR-1Ligand/IonSTRONTIUM ION
12ZN-1Ligand/IonZINC ION
Biological Unit 3 (8, 20)
No.NameCountTypeFull Name
18MC2Mod. Amino Acid(7-METHOXY-2-OXO-2H-CHROMEN-4-YL)ACETIC ACID
2AZI2Ligand/IonAZIDE ION
3CA-1Ligand/IonCALCIUM ION
4DNW2Mod. Amino Acid3-[(2,4-DINITROPHENYL)AMINO]-L-ALANINE
5EDO7Ligand/Ion1,2-ETHANEDIOL
6GOL1Ligand/IonGLYCEROL
7NA-1Ligand/IonSODIUM ION
8NH22Mod. Amino AcidAMINO GROUP
9PFF2Mod. Amino Acid4-FLUORO-L-PHENYLALANINE
10PGO2Ligand/IonS-1,2-PROPANEDIOL
11SR-1Ligand/IonSTRONTIUM ION
12ZN-1Ligand/IonZINC ION

(-) Sites  (25, 25)

Asymmetric Unit (25, 25)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:189 , HIS A:190 , HIS A:226 , ALA A:227 , HIS A:230 , ZN A:301 , LEU P:3 , GLY P:4 , PFF P:5BINDING SITE FOR RESIDUE AZI P 600
02AC2SOFTWAREHIS A:226 , HIS A:230 , HIS A:236 , GLY P:4 , AZI P:600BINDING SITE FOR RESIDUE ZN A 301
03AC3SOFTWAREHIS A:175 , ASP A:177 , HIS A:190 , HIS A:203BINDING SITE FOR RESIDUE ZN A 302
04AC4SOFTWAREASP A:182 , GLY A:183 , ASP A:185 , LEU A:187 , ASP A:205 , GLU A:208BINDING SITE FOR RESIDUE CA A 303
05AC5SOFTWAREASP A:165 , GLY A:197 , GLN A:199 , ASP A:201 , HOH A:414 , HOH A:562 , HOH A:581BINDING SITE FOR RESIDUE SR A 304
06AC6SOFTWAREASP A:131 , ASP A:206 , GLU A:208 , PGO A:312 , HOH A:577BINDING SITE FOR RESIDUE CA A 305
07AC7SOFTWARELYS A:115 , ARG A:265 , LEU A:267 , GLY A:269 , PHE B:107BINDING SITE FOR RESIDUE EDO A 306
08AC8SOFTWARELEU A:114 , GLY A:233 , LEU A:234 , ASP A:235 , HOH A:425BINDING SITE FOR RESIDUE GOL A 307
09AC9SOFTWARELEU A:187 , HIS A:190 , HOH A:411 , PRO P:2BINDING SITE FOR RESIDUE EDO A 308
10BC1SOFTWAREALA A:242 , LEU A:243 , ARG A:249 , HOH A:446 , HOH A:447 , HOH A:557 , PFF P:5BINDING SITE FOR RESIDUE EDO A 309
11BC2SOFTWARELYS A:115 , TRP A:116 , HIS A:117 , HIS A:118 , EDO A:311 , HOH A:438 , HOH A:589BINDING SITE FOR RESIDUE EDO A 310
12BC3SOFTWAREGLY A:195 , PRO A:196 , EDO A:310 , HOH A:448BINDING SITE FOR RESIDUE EDO A 311
13BC4SOFTWAREASP A:131 , GLY A:197 , ASP A:207 , GLU A:208 , LEU A:209 , CA A:305 , HOH A:450 , HOH A:518 , HOH A:576BINDING SITE FOR RESIDUE PGO A 312
14BC5SOFTWAREALA B:189 , HIS B:190 , HIS B:226 , ALA B:227 , HIS B:230 , ZN B:301 , LEU Q:3 , GLY Q:4 , PFF Q:5BINDING SITE FOR RESIDUE AZI Q 600
15BC6SOFTWAREHIS B:226 , HIS B:230 , HIS B:236 , GLY Q:4 , AZI Q:600BINDING SITE FOR RESIDUE ZN B 301
16BC7SOFTWAREHIS B:175 , ASP B:177 , HIS B:190 , HIS B:203BINDING SITE FOR RESIDUE ZN B 302
17BC8SOFTWAREASP B:182 , GLY B:183 , ASP B:185 , LEU B:187 , ASP B:205 , GLU B:208BINDING SITE FOR RESIDUE CA B 303
18BC9SOFTWAREALA B:164 , ASP B:165 , GLY B:197 , GLN B:199 , ASP B:201 , HOH B:448 , HOH B:451BINDING SITE FOR RESIDUE SR B 304
19CC1SOFTWAREASP B:131 , ASP B:206 , GLU B:208 , PGO B:306 , HOH B:420BINDING SITE FOR RESIDUE SR B 305
20CC2SOFTWAREASP B:131 , LYS B:184 , ASP B:206 , ASP B:207 , GLU B:208 , LEU B:209 , SR B:305 , HOH B:500 , HOH B:574BINDING SITE FOR RESIDUE PGO B 306
21CC3SOFTWARETYR B:179 , HIS B:190 , HOH B:491 , PRO Q:2BINDING SITE FOR RESIDUE EDO B 307
22CC4SOFTWAREHIS B:119BINDING SITE FOR RESIDUE EDO B 308
23CC5SOFTWAREPRO A:255 , HOH A:432 , PRO B:255 , HOH B:402 , HOH B:464 , HOH B:593BINDING SITE FOR RESIDUE NA B 309
24CC6SOFTWAREHOH B:433 , HOH B:434 , HOH B:435 , HOH B:510 , HOH B:584BINDING SITE FOR RESIDUE NA B 310
25CC7SOFTWAREHIS B:117 , HIS B:118BINDING SITE FOR RESIDUE NA B 311

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4JQG)

(-) 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:164
                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeee.......hhhhhhhhhhhhhhhhhhh...eeee.......eeeeee...............eeeee..........eeee....ee......eehhhhhhhhhhhhh........................hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jqg A 106 GFQTFEGDLKWHHHNITYWIQNYSEDLPRAVIDDAFARAFALWSAVTPLTFTRVYSRDADIVIQFGVAEHGDGYPFDGKDGLLAHAFPPGPGIQGDAHFDDDELWSLGKGVGYSLFLVAAHAFGHALGLDHSSVPEALMYPMYRFTEGPPLHKDDVNGIRHLYG 269
                                   115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265    


Chain B from PDB  Type:PROTEIN  Length:164
                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeee.......hhhhhhhhhhhhhhhhhhh...eeee.......eeeeee...............eeeee..........eeee....ee......eehhhhhhhhhhhhhh.......................hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jqg B 106 GFQTFEGDLKWHHHNITYWIQNYSEDLPRAVIDDAFARAFALWSAVTPLTFTRVYSRDADIVIQFGVAEHGDGYPFDGKDGLLAHAFPPGPGIQGDAHFDDDELWSLGKGVGYSLFLVAAHAFGHALGLDHSSVPEALMYPMYRFTEGPPLHKDDVNGIRHLYG 269
                                   115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265    


Chain P from PDB  Type:PROTEIN  Length:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ..eeee... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 4jqg P   1 xPLGfaARx   9
                            |   ||  |
                            1-8MC|  |
                                5-PFF
                                 6-DNW
                                    9-NH2


Chain Q from PDB  Type:PROTEIN  Length:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ..eeee... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 4jqg Q   1 xPLGfaARx   9
                            |   ||  |
                            |   ||  |
                            1-8MC|  |
                                5-PFF
                                 6-DNW
                                    9-NH2
   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 4JQG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (38, 38)

Asymmetric Unit(hide GO term definitions)

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  MMP9_HUMAN | P14780
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 Related Entries

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UniProtKB/Swiss-Prot
        MMP9_HUMAN | P14780: 1gkc 1gkd 1itv 1l6j 1lkg 2ovx 2ovz 2ow0 2ow1 2ow2 4h1q 4h2e 4h3x 4h82 4hma 4jij 4wzv 4xct 5cuh 5i12 5th6 5th9

(-) Related Entries Specified in the PDB File

2ow0 MMP-9 ACTIVE SITE MUTANT WITH IODINE-LABELED CARBOXYLATE INHIBITOR
2ow1 MMP-9 ACTIVE SITE MUTANT WITH TRIFLUOROMETHYL HYDROXAMATE INHIBITOR
4h1q CRYSTAL STRUCTURE OF AN MMP TWIN INHIBITOR COMPLEXING TWO MMP-9 CATALYTIC DOMAINS STRUCTURE OF AN MMP TWIN INHIBITOR COMPLEXING TWO MMP-9 CATALYTIC DOMAINS
4h2e CRYSTALCRYSTAL STRUCTURE OF AN MMP TWIN INHIBITOR COMPLEXING TWO MMP-9 CATALYTIC DOMAINS STRUCTURE OF AN MMP TWIN INHIBITOR COMPLEXING TWO MMP-9 CATALYTIC DOMAINS
4h3x CRYSTAL STRUCTURE OF AN MMP BROAD SPECTRUM HYDROXAMATE BASED INHIBITOR CC27 IN COMPLEX WITH THE MMP-9 CATALYTIC DOMAIN
4h82 CRYSTAL STRUCTURE OF MUTANT MMP-9 CATALYTIC DOMAIN IN COMPLEX WITH A TWIN INHIBITOR.
4hma CRYSTAL STRUCTURE OF AN MMP TWIN CARBOXYLATE BASED INHIBITOR LC20 IN COMPLEX WITH THE MMP-9 CATALYTIC DOMAIN
4jij CRYSTAL STRUCTURE OF AN INACTIVE MUTANT OF MMP-9 CATALYTIC DOMAIN IN COMPLEX WITH A FLUOROGENIC SYNTHETIC PEPTIDIC SUBSTRATE
4jxa