Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
(-)Biological Unit 3
collapse expand < >
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)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF U-BOX 2 OF LUBX / LEGU2 / LPP2887 FROM LEGIONELLA PNEUMOPHILA STR. PARIS, ILE175MET MUTANT
 
Authors :  P. J. Stogios, A. T. Qualie, T. Skarina, B. Nocek, R. Di Leo, V. Yim, A. Sa A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)
Date :  18 Nov 14  (Deposition) - 28 Jan 15  (Release) - 19 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.41
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Alpha/Beta Protein, Effector, Structural Genomics, Psi-Biology, Midwest Center For Structural Genomics, Mcsg, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. T. Quaile, M. L. Urbanus, P. J. Stogios, B. Nocek, T. Skarina, A. W. Ensminger, A. Savchenko
Molecular Characterization Of Lubx: Functional Divergence O The U-Box Fold By Legionella Pneumophila.
Structure V. 23 1459 2015
PubMed-ID: 26146184  |  Reference-DOI: 10.1016/J.STR.2015.05.020

(-) Compounds

Molecule 1 - E3 UBIQUITIN-PROTEIN LIGASE LUBX
    Chains: A, B, C
    EC Number: 6.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: P15TV-LIC
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: LUBX, LPP2887
    Mutation: YES
    Organism Scientific: LEGIONELLA PNEUMOPHILA
    Organism Taxid: 297246
    Strain: PARIS
    Synonym: LEGIONELLA U-BOX PROTEIN

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric Unit (3, 9)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2HEZ4Ligand/IonHEXANE-1,6-DIOL
3MSE3Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2HEZ1Ligand/IonHEXANE-1,6-DIOL
3MSE1Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2HEZ3Ligand/IonHEXANE-1,6-DIOL
3MSE1Mod. Amino AcidSELENOMETHIONINE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2HEZ-1Ligand/IonHEXANE-1,6-DIOL
3MSE1Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:180 , ASP A:182 , PHE C:193 , TYR C:194binding site for residue HEZ A 301
2AC2SOFTWAREGLN A:187 , GLN B:187binding site for residue CL A 302
3AC3SOFTWAREGLN A:186 , GLN A:187 , PHE A:193 , TYR A:194 , VAL B:180 , PHE B:181 , ASP B:182binding site for residue HEZ B 301
4AC4SOFTWARETYR B:194 , ARG B:195 , GLU B:198 , TYR C:194 , ARG C:197binding site for residue HEZ B 302
5AC5SOFTWAREGLN B:186 , PHE B:193 , TYR B:194 , HOH B:402 , VAL C:180 , ASP C:182 , GLN C:187binding site for residue HEZ B 303
6AC6SOFTWAREGLN C:187 , HOH C:402binding site for residue CL C 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4WZ2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4WZ2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4WZ2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4WZ2)

(-) Exons   (0, 0)

(no "Exon" information available for 4WZ2)

(-) 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:75
                                                                                                           
               SCOP domains --------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh..........eee.....eeehhhhhhhhhhhh.........hhhhheehhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                 4wz2 A 124 TEIPDIFLCPISKTLIKTPVITAQGKVYDQEALSNFLIATGNKDETGKKLSmDDVVVFDELYQQIKVYNFYRKRE 198
                                   133       143       153       163       173 |     183       193     
                                                                             175-MSE                   


Chain B from PDB  Type:PROTEIN  Length:75
                                                                                                           
               SCOP domains --------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh..........eee.....eeehhhhhhhhhhh..........hhhhheehhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                 4wz2 B 124 TEIPDIFLCPISKTLIKTPVITAQGKVYDQEALSNFLIATGNKDETGKKLSmDDVVVFDELYQQIKVYNFYRKRE 198
                                   133       143       153       163       173 |     183       193     
                                                                             175-MSE                   


Chain C from PDB  Type:PROTEIN  Length:74
                                                                                                          
               SCOP domains -------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh..........eee.....eeehhhhhhhhhhhh..............eehhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                 4wz2 C 124 TEIPDIFLCPISKTLIKTPVITAQGKVYDQEALSNFLIATGNKDETGKKLSmDDVVVFDELYQQIKVYNFYRKR 197
                                   133       143       153       163       173 |     183       193    
                                                                             175-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 4WZ2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4WZ2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4WZ2)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)

 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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    HEZ  [ 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
(no "Cis Peptide Bonds" information available for 4wz2)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ 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 | Biol. Unit 3 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
  4wz2
    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
  LUBX_LEGPA | Q5X159
    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)
  6.3.2.-
    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
  LUBX_LEGPA | Q5X159
    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
        LUBX_LEGPA | Q5X159: 4wz0 4wz3 4xi1

(-) Related Entries Specified in the PDB File

4wz0 U-BOX 1 RELATED ID: MCSG-APC108251 RELATED DB: TARGETTRACK
4wz1 U-BOX 2 (WILD-TYPE)
4wz3 U-BOX 1 IN COMPLEX WITH UBE2D2