Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym.Unit - manually
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asym.Unit - manually
Asym.Unit - manually  (Jmol Viewer)
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 :  CRYSTAL STRUCTURE OF THE ZINC-BETA-LACTAMASE L1 FROM STENOTROPHOMONAS MALTOPHILIA (INHIBITOR 1)
 
Authors :  L. Nauton, G. Garau, R. Kahn, O. Dideberg
Date :  22 Mar 06  (Deposition) - 27 Mar 07  (Release) - 01 Jul 08  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Nauton, R. Kahn, G. Garau, J. F. Hernandez, O. Dideberg
Structural Insights Into The Design Of Inhibitors For The L1 Metallo-Beta-Lactamase From Stenotrophomonas Maltophilia.
J. Mol. Biol. V. 375 257 2008
PubMed-ID: 17999929  |  Reference-DOI: 10.1016/J.JMB.2007.10.036
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - METALLO-BETA-LACTAMASE L1
    Cellular Location: PERIPLASM
    Chains: A, B
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET26
    Expression System Strain: BL21(DE3) PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: L1
    Organism Scientific: STENOTROPHOMONAS MALTOPHILIA
    Organism Taxid: 40324
    Strain: IID 1275
    Synonym: BETA-LACTAMASE TYPE II, PENICILLINASE

 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, 14)

Asymmetric Unit (3, 14)
No.NameCountTypeFull Name
1SO48Ligand/IonSULFATE ION
2VI2Ligand/Ion1,3-DIPHENYL-1H-PYRAZOLE-4,5-DICARBOXYLIC ACID
3ZN4Ligand/IonZINC ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION
2VI-1Ligand/Ion1,3-DIPHENYL-1H-PYRAZOLE-4,5-DICARBOXYLIC ACID
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION
2VI-1Ligand/Ion1,3-DIPHENYL-1H-PYRAZOLE-4,5-DICARBOXYLIC ACID
3ZN-1Ligand/IonZINC ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:116 , HIS A:118 , HIS A:196 , ZN A:402 , VI A:1410BINDING SITE FOR RESIDUE ZN A 401
02AC2SOFTWAREASP A:120 , HIS A:121 , HIS A:263 , ZN A:401 , VI A:1410 , HOH A:1470BINDING SITE FOR RESIDUE ZN A 402
03AC3SOFTWAREHIS B:116 , HIS B:118 , HIS B:196 , ZN B:402 , VI B:2410BINDING SITE FOR RESIDUE ZN B 401
04AC4SOFTWAREASP B:120 , HIS B:121 , HIS B:263 , ZN B:401 , VI B:2410BINDING SITE FOR RESIDUE ZN B 402
05AC5SOFTWAREARG A:252 , LYS A:297 , ARG B:209 , ALA B:275 , ALA B:289 , GLY B:290 , ALA B:291 , HOH B:2569BINDING SITE FOR RESIDUE SO4 B 1001
06AC6SOFTWAREARG A:172 , VAL A:179 , ILE A:180 , THR A:181 , SO4 A:1008BINDING SITE FOR RESIDUE SO4 A 1002
07AC7SOFTWAREARG A:209 , ALA A:275 , ALA A:289 , GLY A:290 , ALA A:291 , HOH A:1602 , HOH A:1615 , ARG B:252 , LYS B:297BINDING SITE FOR RESIDUE SO4 A 1003
08AC8SOFTWAREARG B:102 , GLY B:211 , HOH B:2624BINDING SITE FOR RESIDUE SO4 B 1004
09AC9SOFTWAREARG B:172 , VAL B:179 , ILE B:180 , THR B:181 , HOH B:2494 , HOH B:2604BINDING SITE FOR RESIDUE SO4 B 1005
10BC1SOFTWAREARG A:252 , ARG B:209BINDING SITE FOR RESIDUE SO4 B 1006
11BC2SOFTWAREARG A:102 , HOH A:1524 , HOH A:1557BINDING SITE FOR RESIDUE SO4 A 1007
12BC3SOFTWAREARG A:110 , ARG A:172 , ILE A:180 , THR A:181 , VAL A:182 , SO4 A:1002BINDING SITE FOR RESIDUE SO4 A 1008
13BC4SOFTWARETRP A:39 , HIS A:116 , HIS A:118 , ASP A:120 , HIS A:121 , ILE A:162 , HIS A:196 , SER A:225 , PRO A:227 , HIS A:263 , ZN A:401 , ZN A:402 , HOH A:1470BINDING SITE FOR RESIDUE VI A 1410
14BC5SOFTWARETRP B:39 , HIS B:116 , HIS B:118 , ASP B:120 , HIS B:121 , ILE B:162 , HIS B:196 , SER B:225 , PRO B:227 , HIS B:263 , ZN B:401 , ZN B:402BINDING SITE FOR RESIDUE VI B 2410

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:256 -A:296
2B:256 -B:296

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2GFJ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2GFJ)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BETA_LACTAMASE_B_1PS00743 Beta-lactamases class B signature 1.BLA1_STEMA102-122
 		  2A:113-133
B:113-133
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BETA_LACTAMASE_B_1PS00743 Beta-lactamases class B signature 1.BLA1_STEMA102-122
 		  1A:113-133
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BETA_LACTAMASE_B_1PS00743 Beta-lactamases class B signature 1.BLA1_STEMA102-122
 		  1-
B:113-133

(-) Exons   (0, 0)

(no "Exon" information available for 2GFJ)

(-) 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:266
 aligned with BLA1_STEMA | P52700 from UniProtKB/Swiss-Prot  Length:290

    Alignment length:266
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282      
           BLA1_STEMA    23 EVPLPQLRAYTVDASWLQPMAPLQIADHTWQIGTEDLTALLVQTPDGAVLLDGGMPQMASHLLDNMKARGVTPRDLRLILLSHAHADHAGPVAELKRRTGAKVAANAESAVLLARGGSDDLHFGDGITYPPANADRIVMDGEVITVGGIVFTAHFMAGHTPGSTAWTWTDTRNGKPVRIAYADSLSAPGYQLQGNPRYPHLIEDYRRSFATVRALPCDVLLTPHPGASNWDYAAGARAGAKALTCKAYADAAEQKFDGQLAKETAG 288
               SCOP domains d2gfja_ A: Zn metallo-beta-lactamase                                                                                                                                                                                                                                       SCOP domains
               CATH domains 2gfjA00 A:24-317 Metallo-beta-lactamase, chain A                                                                                                                                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhh....eeee..eee........eeeee..eeeee...hhhhhhhhhhhhhhh..hhh.eeeee....hhhhhhhhhhhhhhh..eeeehhhhhhhhhh....................ee.....eeee..eeeeeee........eeeeeeeee..eeeeeee..................hhhhhhhhhhhhhhh....eee..hhhhhh.hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------BETA_LACTAMASE_B_1   ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gfj A  24 EVPLPQLRAYTVDASWLQPMAPLQIADHTWQIGTEDLTALLVQTPDGAVLLDGGMPQMASHLLDNMKARGVTPRDLRLILLSHAHADHAGPVAELKRRTGAKVAANAESAVLLARGGSDDLHFGDGITYPPANADRIVMDGEVITVGGIVFTAHFMAGHTPGSTAWTWTDTRNGKPVRIAYADSLSAPGYQLQGNPRYPHLIEDYRRSFATVRALPCDVLLTPHPGASNWDYAAGARAGAKALTCKAYADAAEQKFDGQLAKETAG 317
                                    33        43        53   ||   72        82    ||  93       103       113       123       133       143       153   ||  165||     176       186    || 197       207       217    || 229       239       249       259       269      |291       301       311      
                                                            57|                  87|                                                                 157|   166|                    191|                          222|                                                276|                            
                                                             67                   89                                                                  160    168                     193                           225                                                 289                            


Chain B from PDB  Type:PROTEIN  Length:266
 aligned with BLA1_STEMA | P52700 from UniProtKB/Swiss-Prot  Length:290

    Alignment length:266
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282      
           BLA1_STEMA    23 EVPLPQLRAYTVDASWLQPMAPLQIADHTWQIGTEDLTALLVQTPDGAVLLDGGMPQMASHLLDNMKARGVTPRDLRLILLSHAHADHAGPVAELKRRTGAKVAANAESAVLLARGGSDDLHFGDGITYPPANADRIVMDGEVITVGGIVFTAHFMAGHTPGSTAWTWTDTRNGKPVRIAYADSLSAPGYQLQGNPRYPHLIEDYRRSFATVRALPCDVLLTPHPGASNWDYAAGARAGAKALTCKAYADAAEQKFDGQLAKETAG 288
               SCOP domains d2gfjb_ B: Zn metallo-beta-lactamase                                                                                                                                                                                                                                       SCOP domains
               CATH domains 2gfjB00 B:24-317 Metallo-beta-lactamase, chain A                                                                                                                                                                                                                           CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............hhhhhh....ee....eee........eeeee..eeeee...hhhhhhhhhhhhhhh..hhh.eeeee....hhhhhhhhhhhhhhh..eeeehhhhhhhhhh....................ee.....eeee..eeeeeee........eeeeeeeee..eeeeeee..................hhhhhhhhhhhhhhh....eee..hhhhhh.hhhhh........hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------BETA_LACTAMASE_B_1   ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gfj B  24 EVPLPQLRAYTVDASWLQPMAPLQIADHTWQIGTEDLTALLVQTPDGAVLLDGGMPQMASHLLDNMKARGVTPRDLRLILLSHAHADHAGPVAELKRRTGAKVAANAESAVLLARGGSDDLHFGDGITYPPANADRIVMDGEVITVGGIVFTAHFMAGHTPGSTAWTWTDTRNGKPVRIAYADSLSAPGYQLQGNPRYPHLIEDYRRSFATVRALPCDVLLTPHPGASNWDYAAGARAGAKALTCKAYADAAEQKFDGQLAKETAG 317
                                    33        43        53   ||   72        82    ||  93       103       113       123       133       143       153   ||  165||     176       186    || 197       207       217    || 229       239       249       259       269      |291       301       311      
                                                            57|                  87|                                                                 157|   166|                    191|                          222|                                                276|                            
                                                             67                   89                                                                  160    168                     193                           225                                                 289
   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  (0, 0)

(no "Pfam Domain" information available for 2GFJ)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (BLA1_STEMA | P52700)
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.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0017001    antibiotic catabolic process    The chemical reactions and pathways resulting in the breakdown of antibiotic, a substance produced by or derived from certain fungi, bacteria, and other organisms, that can destroy or inhibit the growth of other microorganisms.
    GO:0046677    response to antibiotic    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
cellular component
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).

 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
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    VI  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2gfj)
 
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
  2gfj
    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
  BLA1_STEMA | P52700
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
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
  BLA1_STEMA | P52700
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        BLA1_STEMA | P52700: 1sml 2aio 2fm6 2fu6 2fu7 2fu8 2fu9 2gfk 2h6a 2hb9 2qdt 2qin 2qjs 5dpx 5evb 5evd 5evk 5hh5 5hh6

(-) Related Entries Specified in the PDB File

2gfk