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 :  TOTAL CHEMICAL SYNTHESIS, REFOLDING AND CRYSTALLOGRAPHIC STRUCTURE OF A FULLY ACTIVE IMMUNOPHILIN: CALSTABIN 2 (FKBP12.6).
 
Authors :  S. Sirigu, T. Huet, M. Bacchi, M. Jullian, B. Fould, G. Ferry, L. Vuillar L. Chavas, K. Puget, O. Nosjean, J. A. Boutin
Date :  14 Jan 16  (Deposition) - 05 Oct 16  (Release) - 30 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Synthetic Protein, Refolding, Immunophilin, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Bacchi, M. Jullian, S. Sirigu, B. Fould, T. Huet, L. Bruyand, M. Antoine, L. Vuillard, L. Ronga, L. M. Chavas, O. Nosjean, G. Ferry, K. Puget, J. A. Boutin
Total Chemical Synthesis, Refolding, And Crystallographic Structure Of Fully Active Immunophilin Calstabin 2 (Fkbp12. 6).
Protein Sci. V. 25 2225 2016
PubMed-ID: 27670942  |  Reference-DOI: 10.1002/PRO.3051

(-) Compounds

Molecule 1 - PEPTIDYL-PROLYL CIS-TRANS ISOMERASE FKBP1B
    Chains: A
    EC Number: 5.2.1.8
    Engineered: YES
    Expression System: SYNTHETIC CONSTRUCT
    Expression System Taxid: 32630
    Gene: FKBP1B, FKBP12.6, FKBP1L, FKBP9, OTK4
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PPIASE FKBP1B,12.6 KDA FK506-BINDING PROTEIN,FKBP-12.6, FK506-BINDING PROTEIN 1B,FKBP-1B,IMMUNOPHILIN FKBP12.6,ROTAMASE,H- FKBP-12

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2EDO4Ligand/Ion1,2-ETHANEDIOL
3RAP1Ligand/IonRAPAMYCIN IMMUNOSUPPRESSANT DRUG

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:5 , THR A:6 , TYR A:26 , THR A:27 , MET A:29 , LYS A:35 , PHE A:36 , ASP A:37 , PHE A:46 , GLN A:53 , GLU A:54 , VAL A:55 , ILE A:56 , PHE A:59 , TYR A:82 , ASP A:100 , EDO A:205 , HOH A:317 , HOH A:326 , HOH A:340 , HOH A:375 , HOH A:397binding site for residue RAP A 201
2AC2SOFTWAREHIS A:25 , ASN A:43binding site for residue CL A 202
3AC3SOFTWARELYS A:35binding site for residue CL A 203
4AC4SOFTWAREHOH A:442binding site for residue CL A 204
5AC5SOFTWARESER A:39 , ARG A:42 , LYS A:44 , PHE A:46 , LYS A:73 , RAP A:201 , HOH A:352 , HOH A:387binding site for residue EDO A 205
6AC6SOFTWARETHR A:14 , GLN A:20 , LEU A:68 , HOH A:301 , HOH A:303binding site for residue EDO A 206
7AC7SOFTWARETYR A:82 , ALA A:84 , THR A:85 , EDO A:208 , HOH A:304 , HOH A:386binding site for residue EDO A 207
8AC8SOFTWAREPHE A:15 , PRO A:78 , ASP A:79 , GLY A:83 , ALA A:84 , ASN A:94 , EDO A:207 , HOH A:304 , HOH A:310binding site for residue EDO A 208

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5HKG)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5HKG)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5HKG)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5HKG)

(-) Exons   (0, 0)

(no "Exon" information available for 5HKG)

(-) 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:107
                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee............eeeeeeeeee....eeee.......eeee......hhhhhhhhhh.....eeeeee.hhhh...............eeeeeeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 5hkg A   1 GVEIETISPGDGRTFPKKGQTCVVHYTGMLQNGKKFDSSRDRNKPFKFRIGKQEVIKGFEEGAAQMSLGQRAKLTCTPDVAYGATGHPGVIPPNATLIFDVELLNLE 107
                                    10        20        30        40        50        60        70        80        90       100
   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 5HKG)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5HKG)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5HKG)

(-) Gene Ontology  (50, 50)

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 ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    RAP  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5hkg)
 

(-) 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
  5hkg
    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
  FKB1B_HUMAN | P68106
    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)
  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
  FKB1B_HUMAN | P68106
    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
        FKB1B_HUMAN | P68106: 1c9h 4c02 4iq2 4iqc 5t15 5t9m 5t9n 5t9r 5t9s 5t9v 5ta3 5tal 5tam 5tan 5tap 5taq 5tas 5tat 5tau 5tav 5taw 5tax 5tay 5taz 5tb0 5tb1 5tb2 5tb3 5tb4

(-) Related Entries Specified in the PDB File

1c9h