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

(-) Description

Title :  OXA-48 BETA-LACTAMASE - S70A MUTANT
 
Authors :  V. Stojanoski, C. J. Adamski, L. Hu, S. C. Mehta, B. Sankaran, B. V. V. Pra T. G. Palzkill
Date :  30 Dec 15  (Deposition) - 07 Sep 16  (Release) - 29 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.89
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase, Serine Beta-Lactamase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Stojanoski, C. J. Adamski, L. Hu, S. C. Mehta, B. Sankaran, P. Zwart, B. V. Prasad, T. Palzkill
Removal Of The Side Chain At The Active-Site Serine By A Glycine Substitution Increases The Stability Of A Wide Rang Of Serine Beta-Lactamases By Relieving Steric Strain.
Biochemistry V. 55 2479 2016
PubMed-ID: 27073009  |  Reference-DOI: 10.1021/ACS.BIOCHEM.6B00056

(-) Compounds

Molecule 1 - BETA-LACTAMASE
    Chains: A, B
    EC Number: 3.5.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET29A
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Fragment: UNP RESIDUES 25-265
    Gene: BLA OXA-48, BLAOXA-48, KPE71T_00045
    Mutation: YES
    Organism Scientific: KLEBSIELLA PNEUMONIAE
    Organism Taxid: 573

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (9, 22)

Asymmetric/Biological Unit (9, 22)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2CL1Ligand/IonCHLORIDE ION
3EDO4Ligand/Ion1,2-ETHANEDIOL
4KCX2Mod. Amino AcidLYSINE NZ-CARBOXYLIC ACID
5MPD1Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
6NA2Ligand/IonSODIUM ION
7PEG8Ligand/IonDI(HYDROXYETHYL)ETHER
8PG41Ligand/IonTETRAETHYLENE GLYCOL
9PGE2Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:206 , HOH A:553 , ARG B:206binding site for residue CL A 301
02AC2SOFTWAREALA A:65 , PRO A:217 , HOH A:468 , ASN B:146 , ASP B:148 , GLY B:161binding site for residue 1PE A 302
03AC3SOFTWAREGLN A:98 , ARG B:134 , LYS B:137binding site for residue PGE A 303
04AC4SOFTWAREARG A:174 , LYS A:175 , HIS A:178 , LYS A:180binding site for residue PGE A 304
05AC5SOFTWAREASN A:63 , HOH A:483 , HOH A:506 , ASN B:63 , HOH B:417binding site for residue NA A 305
06AC6SOFTWAREARG A:128 , HOH A:499 , GLN B:129 , ARG B:134binding site for residue PEG A 306
07AC7SOFTWAREASP A:82 , SER A:184 , ARG A:186 , HOH A:505binding site for residue PEG A 307
08AC8SOFTWAREILE A:102 , THR A:104 , TYR A:117 , HOH A:410 , HOH A:512 , PEG B:303binding site for residue PEG A 308
09AC9SOFTWARELEU A:228 , ASP A:229 , HOH A:402 , HOH A:435 , HOH A:445 , ASN B:110 , ILE B:112 , THR B:113 , LYS B:116binding site for residue PEG A 309
10AD1SOFTWARETRP A:47 , ILE A:170 , SER A:171 , ARG A:174binding site for residue MPD A 310
11AD2SOFTWAREASN B:179 , HOH B:438 , HOH B:468binding site for residue NA B 301
12AD3SOFTWAREARG B:174 , HIS B:178binding site for residue PEG B 302
13AD4SOFTWARETYR A:117 , PEG A:308 , HOH A:410 , ASP B:202 , HOH B:401binding site for residue PEG B 303
14AD5SOFTWARETRP B:47 , ARG B:174binding site for residue PEG B 304
15AD6SOFTWAREASP B:82binding site for residue PG4 B 306
16AD7SOFTWAREGLU B:185binding site for residue EDO B 307
17AD8SOFTWAREASP A:229 , ASP B:108 , ASN B:110 , THR B:113binding site for residue EDO B 308
18AD9SOFTWAREHIS B:178binding site for residue EDO B 309
19AE1SOFTWARETHR B:99binding site for residue EDO B 310

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:216 -Pro A:217
2Glu B:216 -Pro B:217

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5HAP)

(-) Sequences/Alignments

Asymmetric/Biological 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:241
                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee...hhhhhhh....eeeeeee....eeee.hhhhhh....hhhhhhhhhhhhhhhh..................hhhhh...hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhh....hhhhhhhhhhhhhh.....hhhhhhhhhhhheeee....eeeeeeeee......eeeeeeeee....eeeeeeeee..hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hap A  25 WQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPAATFkIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP 265
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264 
                                                                           73-KCX                                                                                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:241
                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee...hhhhhhh....eeeeeee....eeee.hhhhhh.ee.hhhhhhhhhhhhhhhh..................hhhhh...hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhh...eehhhhhhhhhhhhh.....hhhhhhhhhhhheeee....eeeeeeeee......eeeeeeeee....eeeeeeeee..hhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hap B  25 WQENKSWNAHFTEHKSQGVVVLWNENKQQGFTNNLKRANQAFLPAATFkIPNSLIALDLGVVKDEHQVFKWDGQTRDIATWNRDHNLITAMKYSVVPVYQEFARQIGEARMSKMLHAFDYGNEDISGNVDSFWLDGGIRISATEQISFLRKLYHNKLHVSERSQRIVKQAMLTEANGDYIIRAKTGYSTRIEPKIGWWVGWVELDDNVWFFAMNMDMPTSDGLGLRQAITKEVLKQEKIIP 265
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264 
                                                                           73-KCX
   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 5HAP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    1PE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    KCX  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MPD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PEG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PG4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PGE  [ 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 ]
    AD1  [ RasMol ]  +environment [ RasMol ]
    AD2  [ RasMol ]  +environment [ RasMol ]
    AD3  [ RasMol ]  +environment [ RasMol ]
    AD4  [ RasMol ]  +environment [ RasMol ]
    AD5  [ RasMol ]  +environment [ RasMol ]
    AD6  [ RasMol ]  +environment [ RasMol ]
    AD7  [ RasMol ]  +environment [ RasMol ]
    AD8  [ RasMol ]  +environment [ RasMol ]
    AD9  [ RasMol ]  +environment [ RasMol ]
    AE1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Glu A:216 - Pro A:217   [ RasMol ]  
    Glu B:216 - Pro B:217   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites 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
  5hap
    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
  Q6XEC0_KLEPN | Q6XEC0
    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
  Q6XEC0_KLEPN | Q6XEC0
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q6XEC0_KLEPN | Q6XEC0: 3hbr 4s2j 4s2k 4s2n 4s2p 4wmc 5dtk 5dts 5dtt 5dva 5faq 5fas 5fat 5haq

(-) Related Entries Specified in the PDB File

5hai 5haq 5har