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
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)

(-) Description

Title :  STRUCTURE OF LEPTOSPIRA INTERROGANS LRR PROTEIN LIC11098
 
Authors :  W. Shepard, F. A. Saul, A. Haouz, M. Picardeau
Date :  11 Jul 14  (Deposition) - 03 Jun 15  (Release) - 17 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Lrr Protein, Pathogen, Virulence Factor, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Miras, F. Saul, M. Nowakowski, P. Weber, A. Haouz, W. Shepard, M. Picardeau
Structural Characterization Of A Novel Subfamily Of Leucine-Rich Repeat Proteins From The Human Pathogen Leptospira Interrogans.
Acta Crystallogr. , Sect. D V. 71 1351 2015
PubMed-ID: 26057675  |  Reference-DOI: 10.1107/S139900471500704X

(-) Compounds

Molecule 1 - LIC11098
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PDEST17
    Expression System Taxid: 469008
    Expression System Variant: PLYSS
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 30-426
    Gene: LIC_11098
    Organism Scientific: LEPTOSPIRA INTERROGANS SEROGROUP ICTEROHAEMORRHAGIAE SEROVAR COPENHAGENI (STRAIN FIOCRUZ L1-130)
    Organism Taxid: 267671
    Strain: FIOCRUZ L1-130

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 13)

Asymmetric Unit (4, 13)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2MSE2Mod. Amino AcidSELENOMETHIONINE
3SO41Ligand/IonSULFATE ION
4ZN9Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MSE1Mod. Amino AcidSELENOMETHIONINE
3SO4-1Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MSE1Mod. Amino AcidSELENOMETHIONINE
3SO41Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:357 , HOH A:699 , HIS B:357 , HOH B:759binding site for residue ZN A 501
02AC2SOFTWAREHIS A:402 , HOH A:801 , ASP B:310binding site for residue ZN A 502
03AC3SOFTWAREASP A:310 , HIS B:402 , HOH B:789binding site for residue ZN A 503
04AC4SOFTWAREASP A:218 , HIS A:239 , HOH A:780 , HOH A:850binding site for residue ZN A 504
05AC5SOFTWAREHIS A:196 , HIS A:219 , HOH A:793 , HOH B:763binding site for residue ZN A 505
06AC6SOFTWAREGLU A:190 , GLU A:213 , HOH A:764 , GLU B:190 , GLU B:213 , HOH B:656binding site for residue CA A 506
07AC7SOFTWAREGLU A:158 , GLU A:161 , LYS A:416 , GLU B:127 , ZN B:503 , HOH B:728binding site for residue SO4 B 501
08AC8SOFTWAREHOH A:817 , HIS B:196 , HIS B:219 , HOH B:782binding site for residue ZN B 502
09AC9SOFTWAREGLU A:158 , GLU B:127 , HIS B:150 , SO4 B:501binding site for residue ZN B 503
10AD1SOFTWAREHOH A:729 , ASP B:80 , HIS B:101 , HOH B:713binding site for residue ZN B 504
11AD2SOFTWAREASP B:218 , HIS B:239 , HOH B:753 , HOH B:812binding site for residue ZN B 505

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4U08)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4U08)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4U08)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4U08)

(-) Exons   (0, 0)

(no "Exon" information available for 4U08)

(-) 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:391
                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.hhhhhhhh.....eee.........hhhhhhh....eee.........hhhhhhh....eee.........hhhhhhh....eee.........hhhhhhh....eee.........hhhhhhh....eee.........hhhhhhh....eee.........hhhhhhh....eee.........hhhhhhh....eee.........hhhhhhh....eee.........hhhhhhh....eee.........hhhhhhh....eee.........hhhhhhh....eee.........hhhhhhh....eee.........hhhhhhh....eee.........hhhhhhh....eee......hhhhhhhhhhhh...eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u08 A  35 QTYYRNITEALKNPQNVRILNLSGSKLTTLPGEIGKLQNLQLLNLDDNQLIALPKEIGKLQNLQQLHLSKNQLmALPEEIGQLQNLQKLKLYENQLTAIPKEIGQLQNLQELNLAHNQLATLPEDIEQLQRLQTLYLGHNQFNSILKEIGQLQNLESLGLDHNQLNVLPKEIGQLRNLESLGLDHNQLNVLPKEIGQLQNLQILHLRNNQLTTLPKEIGQLQNLQKLLLNKNKLTTLPKEIGQLQNLQKLKLYENQLTTLPKEIGQLQNLQELDLDGNQLTTLPENIGQLQRLQTLYLGNNQLNFLPKEIGQLRNLESLDLEHNQLNALPKEIGKLQKLQTLNLKYNQLATLPEEIKQLKNLKKLYLHNNPLPSEKIARIRKLLPQCIIYF 425
                                    44        54        64        74        84        94       104   |   114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424 
                                                                                                   108-MSE                                                                                                                                                                                                                                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:391
                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.hhhhhhhhhhhh.eee.........hhhhhhh....eee.........hhhhhhh....eee.........hhhhhhh....eee.........hhhhhhh....eee.........hhhhhhh....eee.........hhhhhhh....eee.........hhhhhhh....eee.........hhhhhhh....eee.........hhhhhhh....eee.........hhhhhhh....eee.........hhhhhhh....eee.........hhhhhhh....eee.........hhhhhhh....eee.........hhhhhhh....eee.........hhhhhhh....eee......hhhhhhhhhhhh...eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u08 B  35 QTYYRNITEALKNPQNVRILNLSGSKLTTLPGEIGKLQNLQLLNLDDNQLIALPKEIGKLQNLQQLHLSKNQLmALPEEIGQLQNLQKLKLYENQLTAIPKEIGQLQNLQELNLAHNQLATLPEDIEQLQRLQTLYLGHNQFNSILKEIGQLQNLESLGLDHNQLNVLPKEIGQLRNLESLGLDHNQLNVLPKEIGQLQNLQILHLRNNQLTTLPKEIGQLQNLQKLLLNKNKLTTLPKEIGQLQNLQKLKLYENQLTTLPKEIGQLQNLQELDLDGNQLTTLPENIGQLQRLQTLYLGNNQLNFLPKEIGQLRNLESLDLEHNQLNALPKEIGKLQKLQTLNLKYNQLATLPEEIKQLKNLKKLYLHNNPLPSEKIARIRKLLPQCIIYF 425
                                    44        54        64        74        84        94       104   |   114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424 
                                                                                                   108-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 4U08)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4U08)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4U08)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4U08)

 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
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4u08)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ 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 ](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
  4u08
    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
  Q72TC3_LEPIC | Q72TC3
    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
  Q72TC3_LEPIC | Q72TC3
    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 4U08)

(-) Related Entries Specified in the PDB File

4u06 4uo9 4zth