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 :  CRYSTAL STRUCTURE AND FUNCTIONAL CHARACTERIZATION OF THE THERMOPHILIC PROLYL ISOMERASE AND CHAPERONE SLYD
 
Authors :  C. Loew, P. Neumann, U. Weininger, M. T. Stubbs, J. Balbach
Date :  18 Feb 10  (Deposition) - 31 Mar 10  (Release) - 26 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (3x)
Keywords :  Prolyl Cis Trans Isomerase, Chaperone Function, Two Domain Protein, Ni(2+) Zn(2+) Binding, Slyd, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Loew, P. Neumann, H. Tidow, U. Weininger, C. Haupt, B. Friedrich-Epler, C. Scholz, M. T. Stubbs, J. Balbach
Crystal Structure Determination And Functional Characterization Of The Metallochaperone Slyd From Thermus Thermophilus
J. Mol. Biol. V. 398 375 2010
PubMed-ID: 20230833  |  Reference-DOI: 10.1016/J.JMB.2010.03.014

(-) Compounds

Molecule 1 - PEPTIDYL-PROLYL CIS-TRANS ISOMERASE
    Chains: A
    EC Number: 5.2.1.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-VECTOR
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: VECTOR
    Organism Scientific: THERMUS THERMOPHILUS
    Organism Taxid: 300852
    Strain: HB8
 
Molecule 2 - SUC-ALA-LEU-PRO-PHE-PNA
    Chains: B
    Engineered: YES
    Other Details: THE BOUND SUBSTRATE
    Other Details - Source: THE PEPTIDE SUBSTRATE WAS PURCHASED FROM A COMPANY.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (3x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1NIT1Mod. Amino Acid4-NITROANILINE
2SIN1Mod. Amino AcidSUCCINIC ACID
3ZN4Ligand/IonZINC ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1NIT1Mod. Amino Acid4-NITROANILINE
2SIN1Mod. Amino AcidSUCCINIC ACID
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 6)
No.NameCountTypeFull Name
1NIT3Mod. Amino Acid4-NITROANILINE
2SIN3Mod. Amino AcidSUCCINIC ACID
3ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:19 , GLU A:20 , ALA A:52 , GLU A:137 , HOH A:177BINDING SITE FOR RESIDUE ZN A 159
2AC2SOFTWAREHIS A:145 , HIS A:147 , HIS A:149 , HOH A:163BINDING SITE FOR RESIDUE ZN A 160
3AC3SOFTWARETYR A:29 , LEU A:30 , ASN A:35 , HIS A:147 , ALA A:148BINDING SITE FOR RESIDUE ZN A 161
4AC4SOFTWAREGLU A:49BINDING SITE FOR RESIDUE ZN A 162

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3LUO)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Leu B:3 -Pro B:4

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3LUO)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3LUO)

(-) Exons   (0, 0)

(no "Exon" information available for 3LUO)

(-) 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:145
 aligned with Q5SLE7_THET8 | Q5SLE7 from UniProtKB/TrEMBL  Length:149

    Alignment length:151
                                                                                                                                                                              149  
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140        |- 
         Q5SLE7_THET8     1 MKVGQDKVVTIRYTLQVEGEVLDQGELSYLHGHRNLIPGLEEALEGREEGEAFQAHVPAEKAYGPHDPEGVQVVPLSAFPEDAEVVPGAQFYAQDMEGNPMPLTVVAVEGEEVTVDFNHPLAGKDLDFQVEVVKVREATPEELLHGHAH--   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains FKBP_C-3luoA01 A:1-133                                                                                                               ------------------ Pfam domains
         Sec.struct. author ......eeeeeeeeeee..eeeeeeeeeee......hhhhhhhhh......eeeeeehhhhh....hhh.eeeee.hhh.------..eee...........eeeeeee..eeeee.........eeeeeeeeeeee.hhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3luo A   1 MKVGQDKVVTIRYTLQVEGEVLDQGELSYLHGHRNLIPGLEEALEGREEGEAFQAHVPAEKAYGPHDPEGVQVVPLSAFP------PGAQFYAQDMEGNPMPLTVVAVEGEEVTVDFNHPLAGKDLDFQVEVVKVREATPEELLHGHAHPS 151
                                    10        20        30        40        50        60        70        80      | 90       100       110       120       130       140       150 
                                                                                                          80     87                                                                


Chain B from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 3luo B   1 xALPAx   6
                            |    |
                            1-SIN|
                                 6-NIT
   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 3LUO)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3LUO)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: no clan defined [family: FKBP_C] (58)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q5SLE7_THET8 | Q5SLE7)
molecular function
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0003755    peptidyl-prolyl cis-trans isomerase activity    Catalysis of the reaction: peptidyl-proline (omega=180) = peptidyl-proline (omega=0).
biological process
    GO:0006457    protein folding    The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
    GO:0000413    protein peptidyl-prolyl isomerization    The modification of a protein by cis-trans isomerization of a proline residue.

 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
    NIT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SIN  [ 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 ]
 
  Cis Peptide Bonds
    Leu B:3 - Pro B:4   [ RasMol ]  
 
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
  3luo
    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
  Q5SLE7_THET8 | Q5SLE7
    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)
  5.2.1.8
    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
  Q5SLE7_THET8 | Q5SLE7
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q5SLE7_THET8 | Q5SLE7: 3cgm 3cgn 4odk 4odl 4odm 4odn 4odo 4odp 4odq 4odr

(-) Related Entries Specified in the PDB File

3cgm ANOTHER CRYSTAL FORM OF THE SAME PROTEIN
3cgn ANOTHER CRYSTAL FORM OF THE SAME PROTEIN