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(-) Description

Title :  HUMAN CYCLOPHILIN D COMPLEXED WITH AN INHIBITOR
 
Authors :  M. Gelin, L. Colliandre, Y. Bessin, J. F. Guichou
Date :  08 Feb 13  (Deposition) - 19 Feb 14  (Release) - 19 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.32
Chains :  Asym./Biol. Unit :  X
Keywords :  Isomerase-Isomerase Inhibitor Complex Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Ahmed-Belkacem, L. Colliandre, N. Ahnou, Q. Nevers, M. Gelin, Y. Bessin, R. Brillet, O. Cala, D. Douguet, W. Bourguet, I. Krimm, J. M. Pawlotsky, J. F. Guichou
Fragment-Based Discovery Of A New Family Of Non-Peptidic Small-Molecule Cyclophilin Inhibitors With Potent Antiviral Activities.
Nat Commun V. 7 12777 2016
PubMed-ID: 27652979  |  Reference-DOI: 10.1038/NCOMMS12777

(-) Compounds

Molecule 1 - PEPTIDYL-PROLYL CIS-TRANS ISOMERASE F, MITOCHONDRIAL
    Chains: X
    EC Number: 5.2.1.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 44-207
    Gene: CYP3, PPIF
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : X

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
17281Ligand/Ion1-(4-AMINOBENZYL)-3-{2-[(2R)-2-(2-BROMOPHENYL)PYRROLIDIN-1-YL]-2-OXOETHYL}UREA

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG X:97 , MET X:103 , GLN X:105 , GLY X:114 , ARG X:124 , ALA X:143 , ASN X:144 , THR X:149 , GLN X:153 , PHE X:155 , LEU X:164 , HIS X:168 , HOH X:466 , HOH X:548BINDING SITE FOR RESIDUE 728 X 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4J5D)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4J5D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4J5D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4J5D)

(-) Exons   (0, 0)

(no "Exon" information available for 4J5D)

(-) 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 X from PDB  Type:PROTEIN  Length:164
                                                                                                                                                                                                    
               SCOP domains d4j5dx_ X: Mitochondrial peptidyl-prolyl cis-trans isomerase, cyclophilin F                                                                                          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
                 4j5d X  44 GNPLVYLDVDANGKPLGRVVLELKADVVPKTAENFRALCTGEKGFGYKGSTFHRVIPSFMCQAGDFTNHNGTGGKSIYGSRFPDENFTLKHVGPGVLSMANAGPNTNGSQFFICTIKTDWLDGKHVVFGHVIEGMDVVKKIESFGSKSGRTSKKIVITDCGQLS 207
                                    53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203
   Legend:   → Mismatch (orange background)
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  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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4J5D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4J5D)

(-) Gene Ontology  (33, 33)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        PPIF_HUMAN | P30405: 2bit 2biu 2z6w 3qyu 3r49 3r4g 3r54 3r56 3r57 3r59 3rcf 3rcg 3rci 3rck 3rcl 3rd9 3rda 3rdb 3rdc 4j58 4j59 4j5a 4j5b 4j5c 4j5e 4o8h 4o8i 4xnc 4zsc 4zsd 5a0e 5cbt 5cbu 5cbv 5cbw 5ccn 5ccq 5ccr 5ccs

(-) Related Entries Specified in the PDB File

4j58 4j59 4j5a 4j5b 4j5c 4j5e