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 :  HUMAN CYCLOPHILIN D COMPLEXED WITH INHIBITOR
 
Authors :  R. P. Gibson, E. Shore, N. Kershaw, M. Awais, A. Javed, D. Latawiec, S. Pandalaneni, L. Wen, N. Berry, P. O'Neill, R. Sutton, L. Y. Lian
Date :  02 Jul 15  (Deposition) - 20 Jul 16  (Release) - 20 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Cyclophilin, Isomerase, Complex, Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. P. Gibson, E. Shore, N. Kershaw, M. Awais, A. Javed, D. Latawiec, S. Pandalaneni, L. Wen, N. Berry, P. O'Neill, R. Sutton, L. Y. Lian
Human Cyclophilin D Complexed With Inhibitor
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PEPTIDYL-PROLYL CIS-TRANS ISOMERASE F, MITOCHONDRIAL
    ChainsA
    EC Number5.2.1.8
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System Taxid469008
    GenePPIF, CYP3
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPPIASE F,CYCLOPHILIN D,CYPD,CYCLOPHILIN F,MITOCHONDRIAL CYCLOPHILIN,CYP-M,ROTAMASE F

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (6, 6)
No.NameCountTypeFull Name
14ZZ1Ligand/IonETHYL N-{[3-(3-AMINOPYRIDIN-4-YL)BENZYL]CARBAMOYL}GLYCINATE
2FMT1Ligand/IonFORMIC ACID
3K1Ligand/IonPOTASSIUM ION
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
5PG41Ligand/IonTETRAETHYLENE GLYCOL
6PGE1Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPGE A:204binding site for residue K A 201
2AC2SOFTWARECYS A:40 , THR A:41 , LYS A:49 , CYS A:161 , HOH A:322 , HOH A:334 , HOH A:374binding site for residue FMT A 202
3AC3SOFTWAREVAL A:93 , PRO A:95 , HIS A:131 , HOH A:375binding site for residue PG4 A 203
4AC4SOFTWAREPRO A:58 , SER A:59 , TRP A:121 , LYS A:148 , K A:201binding site for residue PGE A 204
5AC5SOFTWAREGLN A:163 , SER A:165binding site for residue PEG A 205
6AC6SOFTWAREARG A:55 , GLN A:63 , GLY A:72 , THR A:73 , ALA A:101 , ASN A:102 , THR A:107 , GLN A:111 , PHE A:113 , HIS A:126 , HOH A:405binding site for residue 4ZZ A 206

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5CCN)

(-) 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:164
                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee..eeeeeeeeee....hhhhhhhhhhhhhh..........eeeee...eeee................................eeee...........eeee...hhhhh....eeeeeeehhhhhhhhhhh..........eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ccn A   2 GNPLVYLDVDANGKPLGRVVLELKADVVPKTAENFRALCTGEKGFGYKGSTFHRVIPSFMCQAGDFTNHNGTGGKSIYGSRFPDENFTLKHVGPGVLSMANAGPNTNGSQFFICTIKTDWLDGKHVVFGHVIEGMDVVKKIESFGSKSGRTSKKIVITDCGQLS 165
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161    

   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 5CCN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (33, 33)

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
    4ZZ  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FMT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    K  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PEG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PG4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PGE  [ 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 5ccn)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5ccn
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PPIF_HUMAN | P30405
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  5.2.1.8
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  PPIF_HUMAN | P30405
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PPIF_HUMAN | P304052bit 2biu 2z6w 3qyu 3r49 3r4g 3r54 3r56 3r57 3r59 3rcf 3rcg 3rci 3rck 3rcl 3rd9 3rda 3rdb 3rdc 4j58 4j59 4j5a 4j5b 4j5c 4j5d 4j5e 4o8h 4o8i 4xnc 4zsc 4zsd 5a0e 5cbt 5cbu 5cbv 5cbw 5ccq 5ccr 5ccs

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5CCN)