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 PSEUDOMONAS AERUGINOSA PBP3 WITH A R4 SUBSTITUTED ALLYL MONOCARBAM
 
Authors :  A. D. Ferguson
Date :  10 Sep 14  (Deposition) - 22 Apr 15  (Release) - 10 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A
Keywords :  Inhibitor, Siderophore-Conjugated Monocarbams, Pseudomonas Aeruginosa, Penicillin-Binding Protein 3 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. E. Murphy-Benenato, B. Dangel, H. E. Davis, T. F. Durand-Reville, A. D. Ferguson, N. Gao, H. Jahic, J. P. Mueller, E. L. Manyak, O. Quiroga M. Rooney, L. Sha, M. Sylvester, F. Wu, M. Zambrowski, S. X. Zhao
Sar And Structural Analysis Of Siderophore-Conjugated Monocarbam Inhibitors Of Pseudomonas Aeruginosa Pbp3.
Acs Med. Chem. Lett. V. 6 537 2015
PubMed-ID: 26005529  |  Reference-DOI: 10.1021/ACSMEDCHEMLETT.5B00026

(-) Compounds

Molecule 1 - PENICILLIN-BINDING PROTEIN 3
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: CIA_00399
    Organism Scientific: PSEUDOMONAS AERUGINOSA PA14
    Organism Taxid: 652611

 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
13LB1Ligand/Ion(3R,4S,7Z)-7-(2-AMINO-1,3-THIAZOL-4-YL)-4-FORMYL-1-[({3-[(5R)-5-HYDROXY-4-OXO-4,5-DIHYDROPYRIDIN-2-YL]-4-[3-(METHYLSULFONYL)PROPYL]-5-OXO-4,5-DIHYDRO-1H-1,2,4-TRIAZOL-1-YL}SULFONYL)AMINO]-10,10-DIMETHYL-1,6-DIOXO-3-(PROP-2-EN-1-YL)-9-OXA-2,5,8-TRIAZAUNDEC-7-EN-11-OICACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:291 , SER A:294 , ARG A:331 , ASP A:332 , VAL A:333 , SER A:334 , SER A:349 , ASN A:351 , GLY A:408 , GLY A:469 , GLY A:470 , VAL A:471 , LYS A:484 , SER A:485 , GLY A:486 , THR A:487 , ALA A:488 , ARG A:489 , TYR A:503 , PHE A:533 , GLY A:534 , GLY A:535 , LEU A:536 , HOH A:771 , HOH A:782 , HOH A:794 , HOH A:851binding site for residue 3LB A 601

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Gln A:265 -Pro A:266
2Tyr A:319 -Pro A:320
3Ala A:511 -Pro A:512

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4WEJ)

(-) 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:500
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee......ee.....eeeeeeeeeeeeehhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhh.....eeeeeeehhhhhhhhhh.....eeeeeeeeee..hhhhhhhhhhee.....eeehhhhhhhhhhhh..eeeeeee..........eeee.......ee...hhhhhhhhhhhhhhhhhhhh..eeeeeeee.....eeeeeee.................hhhhhh...hhhhhhhhhhhhhhhh.......eee....eeee..eeee.......eeehhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh........................hhhhhhhhhh......hhhhhhhhhhhhhh..ee..............ee..hhhhhhhhhhhhhhhhhh...hhhhh......eeeeeeee...eeeeeeeee......eeeeeeee.......hhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wej A  51 RSVRHIAIPAHRGLITDRNGEPLAVSTPVTTLWANPKELMTAKERWPQLAAALGQDTKLFADRIEQNAEREFIYLVRGLTPEQGEGVIALKVPGVYSIEEFRRFYPAGEVVAHAVGFTDVDDRGREGIELAFDEWLAGVPGKRQVLKDRRGRVIKDVQVTKNAKPGKTLALSIDLRLQYLAHRELRNALLENGAKAGSLVIMDVKTGEILAMTNQPTYNPNNRRNLQPAAMRNRAMIDVFEPGSTVKPFSMSAALASGRWKPSDIVDVYPGTLQIGRYTIRDVSRNSRQLDLTGILIKSSNVGISKIAFDIGAESIYSVMQQVGLGQDTGLGFPGERVGNLPNHRKWPKAETATLAYGYGLSVTAIQLAHAYAALANDGKSVPLSMTRVDRVPDGVQVISPEVASTVQGMLQQVVEAQGGVFRAQVPGYHAAGKSGTARKNAYRSLFAGFAPATDPRIAMVVVIDEPSKAGYFGGLVSAPVFSKVMAGALRLMNVPPDNL 560
                                    60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490|      510       520       530       540       550       560
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 490|                                                           
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  501
   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 4WEJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4WEJ)

 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
    3LB  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:511 - Pro A:512   [ RasMol ]  
    Gln A:265 - Pro A:266   [ RasMol ]  
    Tyr A:319 - Pro A:320   [ 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
  4wej
    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
  A0A0M3KKZ3_P | A0A0M3KKZ3
    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)
  (no 'Enzyme Classificator' available)
    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
  A0A0M3KKZ3_P | A0A0M3KKZ3
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        A0A0M3KKZ3_P | A0A0M3KKZ3: 4wel

(-) Related Entries Specified in the PDB File

4wek 4wel