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 :  CRYSTAL STRUCTURE OF PBP1A IN COMPLEX WITH COMPOUND 17 ((4Z,8S,11E, 14S)-5-(2-AMINO-1,3-THIAZOL-4-YL)-14-(5,6-DIHYDROXY-1,3-DIOXO-1,3-DIHYDRO-2H-ISOINDOL-2-YL)-8-FORMYL-2-METHYL-6-OXO-3,10-DIOXA-4,7,11-TRIAZATETRADECA-4,11-DIENE-2,12,14-TRICARBOXYLIC ACID)
 
Authors :  S. Han, N. Caspers, J. D. Knafels
Date :  03 Feb 14  (Deposition) - 07 May 14  (Release) - 21 May 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Pbp1A, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Starr, M. F. Brown, L. Aschenbrenner, N. Caspers, Y. Che, B. S. Gerstenberger, M. Huband, J. D. Knafels, M. M. Lemmon, C. Li, S. P. Mccurdy, E. Mcelroy, M. R. Rauckhorst, A. P. Tomaras, J. A. Young, R. P. Zaniewski, V. Shanmugasundaram, S. Han
Siderophore Receptor-Mediated Uptake Of Lactivicin Analogue In Gram-Negative Bacteria.
J. Med. Chem. V. 57 3845 2014
PubMed-ID: 24694215  |  Reference-DOI: 10.1021/JM500219C

(-) Compounds

Molecule 1 - PENICILLIN-BINDING PROTEIN 1A
    Chains: A
    EC Number: 2.4.2.-, 3.4.-.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: PBP1A: UNP RESIDUES 36-822
    Gene: MRCA, PONA, PA5045
    Organism Scientific: PSEUDOMONAS AERUGINOSA PAO1
    Organism Taxid: 208964
    Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228
    Synonym: PBP-1A, PBP1A, PENICILLIN-INSENSITIVE TRANSGLYCOSYLASE, PEPTIDOGLYCAN TGASE, PENICILLIN-SENSITIVE TRANSPEPTIDASE, DD- TRANSPEPTIDASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
12U41Ligand/Ion(4Z,8S,11E,14S)-5-(2-AMINO-1,3-THIAZOL-4-YL)-14-(5,6-DIHYDROXY-1,3-DIOXO-1,3-DIHYDRO-2H-ISOINDOL-2-YL)-8-FORMYL-2-METHYL-6-OXO-3,10-DIOXA-4,7,11-TRIAZATETRADECA-4,11-DIENE-2,12,14-TRICARBOXYLIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:458 , SER A:461 , SER A:520 , ASN A:522 , LEU A:559 , THR A:680 , THR A:696 , GLY A:697 , THR A:698 , THR A:699 , ASN A:700 , ASP A:701 , TYR A:733 , HOH A:1001 , HOH A:1002BINDING SITE FOR RESIDUE 2U4 A 901

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu A:508 -Gly A:509

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4OON)

(-) 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:502
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....eeeee........hhhhhhhhhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhhhhhhh.......ee....hhhhhhhhhhh......eeeeeeeee...eeeee.....eeeee.hhhh................hhhhhh...eeeeeee.....eeee.....eeeeeee......eeeee...................hhhhhhhhhhhhhhh.......eeee.............eeeehhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh...hhhhh..hhhhhhh....hhhhhhhhhhhhhh.........eeeee.....eeee.................hhhhhhhhhhhhhhhhhh..hhhhhhhh....eeeeee.hhh.eeeeeee....eeeeeee...........hhhhhhhhhhhhhhhhhh.............eeeeee...............eeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4oon A  47 PLKVYSEDGKLISEFGEMTPELNAPYIAEMARAEMVGRYGSEAYTEGYKVITTVRSDLQNAASQSVRDGLIDYDQRHGYRGPETRLPGQTRDAWLKHLGQQRSIGGLEPAIVTQVEKSGIMVMTRDGKEEAVTWDSMKWARPFLSNNSMGPMPRQPADVAQAGDQIRVQRQEDGTLRFVQIPAAQSALISLDPKDGAIRSLVGGFSFEQSNYNRAIQAKRQPGSSFKPFIYSAALDNGFTAASLVNDAPIVFVDEYLTFLGPIPLREALYKSRNMVSIRVLQGLGIERAISYITKFGFQRDELPRNFSLALGTATVTPMEIAGAWSVFANGGYKVNPYVIERIESRDGQVLYQANPPRVPVEPTPAERIIDARTAYIMTSMLQDVIKRGTGRRALALKRTDLAGKTGTTNDSKDGWFSGYNSDYVTSVWVGFDQPETLGRREYGGTVALPIWIRYMGFALKDKPMHTMAEPPGIVSLRIDPVTGRSAAPGTPGAYFEMFKNE 792
                                    56       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487      |508       518       528       538       548       558       568       578       588       598       608||     660       670       680       690       700       710       720       730       740       750       760       770       780       790  
                                            64|                                                                                                                                                                                                                                           494|                                                                                                    609|                                                                                                                                            
                                            256                                                                                                                                                                                                                                            506                                                                                                     652
   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 4OON)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

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
    2U4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Leu A:508 - Gly A:509   [ 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
  4oon
    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
  PBPA_PSEAE | Q07806
    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)
  2.4.2.-
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
  3.4.-.-
    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
  PBPA_PSEAE | Q07806
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 4OON)

(-) Related Entries Specified in the PDB File

4ool 4oom