Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  FEZ-1-Y228A, A MUTANT OF THE METALLO-BETA-LACTAMASE FROM LEGIONELLA GORMANII
 
Authors :  I. Garcia-Saez, P. S. Mercuri, M. Galleni, O. Dideberg
Date :  27 Mar 02  (Deposition) - 01 Jul 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.01
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Monomer With Alpha-Beta/Beta-Alpha Fold, Two Monomers Per Assymmetric Unit, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Garcia-Saez, P. S. Mercuri, C. Papamicael, R. Kahn, J. M. Frre, M. Galleni, G. M. Rossolini, O. Dideberg
Three-Dimensional Structure Of Fez-1, A Monomeric Subclass B3 Metallo-Beta-Lactamase From Fluoribacter Gormanii, In Native Form And In Complex With -Captopril
J. Mol. Biol. V. 325 651 2003
PubMed-ID: 12507470  |  Reference-DOI: 10.1016/S0022-2836(02)01271-8

(-) Compounds

Molecule 1 - FEZ-1 B-LACTAMASE
    Chains: A, B
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: BLAFEZ-1
    Mutation: YES
    Organism Scientific: FLUORIBACTER GORMANII
    Organism Taxid: 464
    Synonym: FEZ-1 PROTEIN

 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  (4, 17)

Asymmetric Unit (4, 17)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2GOL4Ligand/IonGLYCEROL
3SO47Ligand/IonSULFATE ION
4ZN4Ligand/IonZINC ION
Biological Unit 1 (2, 6)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL2Ligand/IonGLYCEROL
3SO44Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 5)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GOL2Ligand/IonGLYCEROL
3SO43Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREZN A:2 , HIS A:116 , HIS A:118 , HIS A:196 , SO4 A:501BINDING SITE FOR RESIDUE ZN A 1
02AC2SOFTWAREZN A:1 , ASP A:120 , HIS A:121 , HIS A:263 , SO4 A:501 , HOH A:645BINDING SITE FOR RESIDUE ZN A 2
03AC3SOFTWAREZN B:2 , HIS B:116 , HIS B:118 , HIS B:196 , SO4 B:503BINDING SITE FOR RESIDUE ZN B 1
04AC4SOFTWAREZN B:1 , ASP B:120 , HIS B:121 , HIS B:263 , SO4 B:503 , HOH B:663BINDING SITE FOR RESIDUE ZN B 2
05AC5SOFTWARETYR A:293BINDING SITE FOR RESIDUE CL A 400
06AC6SOFTWARETYR B:293BINDING SITE FOR RESIDUE CL B 401
07AC7SOFTWARELYS A:100 , LYS A:105 , PHE A:106 , SER A:107BINDING SITE FOR RESIDUE SO4 A 500
08AC8SOFTWAREZN A:1 , ZN A:2 , HIS A:118 , ASP A:120 , HIS A:196 , ASN A:225 , HIS A:263 , HOH A:645BINDING SITE FOR RESIDUE SO4 A 501
09AC9SOFTWARELYS B:100 , LYS B:105 , PHE B:106 , SER B:107BINDING SITE FOR RESIDUE SO4 B 502
10BC1SOFTWAREZN B:1 , ZN B:2 , HIS B:118 , ASP B:120 , HIS B:196 , ASN B:225 , HIS B:263 , HOH B:663BINDING SITE FOR RESIDUE SO4 B 503
11BC2SOFTWARELYS A:212 , TYR A:214 , LYS B:291BINDING SITE FOR RESIDUE SO4 A 505
12BC3SOFTWAREARG B:78 , HIS B:155 , HOH B:661BINDING SITE FOR RESIDUE SO4 B 506
13BC4SOFTWAREARG A:78 , HIS A:155 , HOH A:686BINDING SITE FOR RESIDUE SO4 A 507
14BC5SOFTWAREMET A:137 , LYS A:172 , ARG A:179 , VAL A:180 , GLU A:181 , HOH A:672 , HOH A:741BINDING SITE FOR RESIDUE GOL A 600
15BC6SOFTWARETHR A:188 , HIS A:190 , THR A:204 , MET A:205 , LYS A:206 , GLN A:215 , HOH A:647 , SER B:252BINDING SITE FOR RESIDUE GOL A 601
16BC7SOFTWAREMET B:137 , LYS B:172 , ARG B:179 , VAL B:180 , GLU B:181 , HOH B:680BINDING SITE FOR RESIDUE GOL B 602
17BC8SOFTWARETHR B:188 , HIS B:190 , THR B:204 , MET B:205 , LYS B:206 , GLN B:215 , MET B:254 , HOH B:634 , HOH B:741BINDING SITE FOR RESIDUE GOL B 603

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:256 -A:290
2B:256 -B:290

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1L9Y)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1L9Y)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1L9Y)

(-) Exons   (0, 0)

(no "Exon" information available for 1L9Y)

(-) 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:263
 aligned with Q9K578_9GAMM | Q9K578 from UniProtKB/TrEMBL  Length:282

    Alignment length:263
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279   
         Q9K578_9GAMM    20 AYPMPNPFPPFRIAGNLYYVGTDDLASYLIVTPRGNILINSDLEANVPMIKASIKKLGFKFSDTKILLISHAHFDHAAGSELIKQQTKAKYMVMDEDVSVILSGGKSDFHYANDSSTYFTQSTVDKVLHDGERVELGGTVLTAHLTPGHTRGCTTWTMKLKDHGKQYQAVIIGSIGVNPGYKLVDNITYPKIAEDYKHSIKVLESMRCDIFLGSHAGMFDLKNKYVLLQKGQNNPFVDPTGCKNYIEQKANDFYTELKKQETA 282
               SCOP domains d1l9ya_ A: Zn metallo-beta-lactamase                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1l9yA00 A:35-311 Metallo-beta-lactamase, chain A                                                                                                                                                                                                                        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeee..eee........eeeee..eeeee...hhhhhhhhhhhhhhh..hhh.eeeee....hhhhhhhhhhhhhhhh.eeeee..hhhhhhh..........hhhhh.......eee....eeee..eeeeeee........eeeeeeeee..eeeeeeee..................hhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1l9y A  35 AYPMPNPFPPFRIAGNLYYVGTDDLASYLIVTPRGNILINSDLEANVPMIKASIKKLGFKFSDTKILLISHAHFDHAAGSELIKQQTKAKYMVMDEDVSVILSGGKSDFHYANDSSTYFTQSTVDKVLHDGERVELGGTVLTAHLTPGHTRGCTTWTMKLKDHGKQYQAVIIGSIGVNPGAKLVDNITYPKIAEDYKHSIKVLESMRCDIFLGSHAGMFDLKNKYVLLSKGQNNPFVDPTGCKNYIEQKANDFYTELKKQETG 311
                                    44||      55 ||     73  ||    84  ||    95       105       115       125       135       145       155  ||   166       176       186     ||197       207       217       227       237       247    || 258       268       278       288       298       308   
                                     45|        57|        76|       87|                                                                  158|                             192|                                                       252|                                                         
                                      47         66         78        89                                                                   160                              194                                                        254                                                         


Chain B from PDB  Type:PROTEIN  Length:263
 aligned with Q9K578_9GAMM | Q9K578 from UniProtKB/TrEMBL  Length:282

    Alignment length:263
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279   
         Q9K578_9GAMM    20 AYPMPNPFPPFRIAGNLYYVGTDDLASYLIVTPRGNILINSDLEANVPMIKASIKKLGFKFSDTKILLISHAHFDHAAGSELIKQQTKAKYMVMDEDVSVILSGGKSDFHYANDSSTYFTQSTVDKVLHDGERVELGGTVLTAHLTPGHTRGCTTWTMKLKDHGKQYQAVIIGSIGVNPGYKLVDNITYPKIAEDYKHSIKVLESMRCDIFLGSHAGMFDLKNKYVLLQKGQNNPFVDPTGCKNYIEQKANDFYTELKKQETA 282
               SCOP domains d1l9yb_ B: Zn metallo-beta-lactamase                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1l9yB00 B:35-311 Metallo-beta-lactamase, chain A                                                                                                                                                                                                                        CATH domains
           Pfam domains (1) -------------------Lactamase_B-1l9yB01 B:55-263                                                                                                                                                                        ------------------------------------------------ Pfam domains (1)
           Pfam domains (2) -------------------Lactamase_B-1l9yB02 B:55-263                                                                                                                                                                        ------------------------------------------------ Pfam domains (2)
         Sec.struct. author ..........eeee..eee........eeeee..eeeee...hhhhhhhhhhhhhhh..hhh.eeeee....hhhhhhhhhhhhhhhh.eeeee..hhhhhhh..........hhhhh.......eee....eeee..eeeeeee........eeeeeeeee..eeeeeeee..................hhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1l9y B  35 AYPMPNPFPPFRIAGNLYYVGTDDLASYLIVTPRGNILINSDLEANVPMIKASIKKLGFKFSDTKILLISHAHFDHAAGSELIKQQTKAKYMVMDEDVSVILSGGKSDFHYANDSSTYFTQSTVDKVLHDGERVELGGTVLTAHLTPGHTRGCTTWTMKLKDHGKQYQAVIIGSIGVNPGAKLVDNITYPKIAEDYKHSIKVLESMRCDIFLGSHAGMFDLKNKYVLLSKGQNNPFVDPTGCKNYIEQKANDFYTELKKQETG 311
                                    44||      55 ||     73  ||    84  ||    95       105       115       125       135       145       155  ||   166       176       186     ||197       207       217       227       237       247    || 258       268       278       288       298       308   
                                     45|        57|        76|       87|                                                                  158|                             192|                                                       252|                                                         
                                      47         66         78        89                                                                   160                              194                                                        254
   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  (1, 2)

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

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: Metallo-HOrase (67)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q9K578_9GAMM | Q9K578)
molecular function
    GO:0008800    beta-lactamase activity    Catalysis of the reaction: a beta-lactam + H2O = a substituted beta-amino acid.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
    BC8  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1l9y)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1l9y
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q9K578_9GAMM | Q9K578
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  3.5.2.6
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  Q9K578_9GAMM | Q9K578
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q9K578_9GAMM | Q9K578: 1jt1 1k07

(-) Related Entries Specified in the PDB File

1jt1 FEZ-1 METALLO-BETA-LACTAMASE FROM LEGIONELLA GORMANII MODELED WITH D-CAPTOPRIL
1k07 NATIVE FEZ-1 METALLO-BETA-LACTAMASE FROM LEGIONELLA GORMANII