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 A TRAP PERIPLASMIC SOLUTE BINDING PROTEIN FROM CHROMOHALOBACTER SALEXIGENS DSM 3043 (CSAL_0678), TARGET EFI-501078, WITH BOUND ETHANOLAMINE
 
Authors :  M. W. Vetting, N. F. Al Obaidi, L. L. Morisco, S. R. Wasserman, S. Sojitr M. Stead, J. D. Attonito, A. Scott Glenn, S. Chowdhury, B. Evans, B. Hi J. Love, R. D. Seidel, H. J. Imker, J. A. Gerlt, S. C. Almo, Enzyme Funct Initiative (Efi)
Date :  08 Aug 14  (Deposition) - 03 Sep 14  (Release) - 26 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Trap Periplasmic Solute Binding Family, Enzyme Function Initiative, Efi, Structural Genomics, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. W. Vetting, N. Al-Obaidi, S. Zhao, B. San Francisco, J. Kim, D. J. Wichelecki, J. T. Bouvier, J. O. Solbiati, H. Vu, X. Zhang, D. A. Rodionov, J. D. Love, B. S. Hillerich, R. D. Seidel, R. J. Quinn, A. L. Osterman, J. E. Cronan, M. P. Jacobson, J. A. Gerlt, S. C. Almo
Experimental Strategies For Functional Annotation And Metabolism Discovery: Targeted Screening Of Solute Binding Proteins And Unbiased Panning Of Metabolomes.
Biochemistry V. 54 909 2015
PubMed-ID: 25540822  |  Reference-DOI: 10.1021/BI501388Y

(-) Compounds

Molecule 1 - TWIN-ARGININE TRANSLOCATION PATHWAY SIGNAL
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: CSAL_0678
    Organism Scientific: CHROMOHALOBACTER SALEXIGENS
    Organism Taxid: 290398
    Strain: DSM 3043

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 18)

Asymmetric/Biological Unit (3, 18)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
2ETA2Ligand/IonETHANOLAMINE
3MSE12Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:50 , ALA A:51 , PRO A:53 , ALA A:54 , SER A:271 , HOH A:562binding site for residue CL A 401
2AC2SOFTWARELYS A:134 , ALA A:151 , HOH A:759binding site for residue CL A 402
3AC3SOFTWARETYR A:41 , LEU A:46 , TYR A:113 , TRP A:154 , ASP A:155 , TRP A:215 , SER A:216 , GLU A:220 , TRP A:242binding site for residue ETA A 403
4AC4SOFTWAREVAL B:50 , ALA B:51 , PRO B:53 , ALA B:54 , SER B:271 , HOH B:612binding site for residue CL B 401
5AC5SOFTWARELYS B:134 , SER B:150 , ALA B:151 , HOH B:723binding site for residue CL B 402
6AC6SOFTWARETYR B:41 , LEU B:46 , TYR B:113 , TRP B:154 , ASP B:155 , TRP B:215 , SER B:216 , GLU B:220 , TRP B:242binding site for residue ETA B 403

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Arg A:343 -Pro A:344
2Arg B:343 -Pro B:344

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4UAB)

(-) 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:315
                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee..hhhhhhhhhhhhhhhhhhhhh..eeeeee......hhhhhhhhhhh....eeeehhhhhh....hhhhh..........hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee....eeee.....hhhhhh..eee.hhhhhhhhhhhh.ee...hhhhhhhhhhh....eeeeehhhhhhhhhhhhh..eee........eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4uab A  33 TIKWRmQTYAGAALAEHVAKPAIDLFNRIAGDRmQIELYSADQLVPTGELFRAmQRGTIDAVQSDDDSmASPTEVTVFGGYFPFGCRYSLDVPVLFNQYGLKEIWEEEYAKVGVKHVSAGAWDPCHFATKEPIRSLKDLEGKRVFTFPTAGRFLSRFGVVPVTLPWEDIEVALQTGELDGIAWSGITEDYTVGWANVTNYFLTNNISGAWIGHFFVNmERWEELPEDLRLLFEVCCEQSHYHRQYWYWGGEARLRVHGDKLELTSIPDAEWDQVETAAQEFWDEIAAQSETKAKVVEIFKQYNADmRKAGRPYRY 347
                                 |  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       292       302       312       322       332     | 342     
                                 |                          66-MSE              86-MSE        101-MSE                                                                                                                                              250-MSE                                                                                 338-MSE     
                                38-MSE                                                                                                                                                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:314
                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..hhhhhhhhhhhhhhhhhhhhhhhheeeee......hhhhhhhhhhh....eeee..........hhhhh..........hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee....eeee.....hhhhhh..eee.hhhhhhhhhhhh.eee..hhhhhhhhhhh....eeeeehhhhhhhhhhhhh..eee........eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4uab B  34 IKWRmQTYAGAALAEHVAKPAIDLFNRIAGDRmQIELYSADQLVPTGELFRAmQRGTIDAVQSDDDSmASPTEVTVFGGYFPFGCRYSLDVPVLFNQYGLKEIWEEEYAKVGVKHVSAGAWDPCHFATKEPIRSLKDLEGKRVFTFPTAGRFLSRFGVVPVTLPWEDIEVALQTGELDGIAWSGITEDYTVGWANVTNYFLTNNISGAWIGHFFVNmERWEELPEDLRLLFEVCCEQSHYHRQYWYWGGEARLRVHGDKLELTSIPDAEWDQVETAAQEFWDEIAAQSETKAKVVEIFKQYNADmRKAGRPYRY 347
                                |   43        53        63  |     73        83  |     93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243      |253       263       273       283       293       303       313       323       333    |  343    
                               38-MSE                      66-MSE              86-MSE        101-MSE                                                                                                                                              250-MSE                                                                                 338-MSE
   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 4UAB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ETA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ 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 ]
 
  Cis Peptide Bonds
    Arg A:343 - Pro A:344   [ RasMol ]  
    Arg B:343 - Pro B:344   [ 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
  4uab
    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
  Q1QZR9_CHRSD | Q1QZR9
    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
  Q1QZR9_CHRSD | Q1QZR9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q1QZR9_CHRSD | Q1QZR9: 4xf5

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4UAB)