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(-) Description

Title :  CRYSTAL STRUCTURE OF CYCLOPHILIN D IN COMPLEX WITH CSA ANALOGUE, JW47.
 
Authors :  J. Warne, G. Pryce, J. Hill, X. Shi, F. Lenneras, F. Puentes, M. Kip, L. Hi P. Walker, M. Simone, A. W. E. Chan, G. Towers, A. R. Coker, M. Duchen, G. Szabadkai, D. Baker, D. L. Selwood
Date :  19 Apr 15  (Deposition) - 30 Dec 15  (Release) - 16 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.25
Chains :  Asym. Unit :  A,B,C,E
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,E  (1x)
Keywords :  Isomerase, Cyclophilin D, Cyp D, Ppif, Cyclosporin A, Csa, Jw47, Mitochondrial Permeability Transition Pore, Ptp, Peptidylprolyl Cis-Trans Isomerase, Cyclophilin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Warne, G. Pryce, J. Hill, X. Shi, F. Lenneras, F. Puentes, M. Kip, L. Hilditch, P. Walker, M. I. Simone, A. W. E. Chan, G. J. Towers, A. R. Coker, M. R. Duchen, G. Szabadkai, D. Baker, D. L. Selwood
Selective Inhibition Of The Mitochondrial Permeability Transition Pore Protects Against Neuro-Degeneration In Experimental Multiple Sclerosis.
J. Biol. Chem. V. 291 4356 2016
PubMed-ID: 26679998  |  Reference-DOI: 10.1074/JBC.M115.700385

(-) Compounds

Molecule 1 - PEPTIDYL-PROLYL CIS-TRANS ISOMERASE F, MITOCHONDRIAL
    Chains: A, B
    EC Number: 5.2.1.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: POPINF
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: PLYSS
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PPIASE F, 5.2.1.8, CYCLOPHILIN D, CYP-D, CYPD, CYCLOPHILIN F, MITOCHONDRIAL CYCLOPHILIN, CYP-M, ROTAMASE F
 
Molecule 2 - JW47
    Chains: C, E
    Organism Scientific: CYLINDROCARPON LUCIDUM
    Organism Taxid: 301100
    Other Details: CYCLOSPORINE A WITH 1-(PENT-4-ENYL) QUINOLINIUM LINKED TO THE BMT RESIDUE.
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCE
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B E

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 18)

Asymmetric Unit (6, 18)
No.NameCountTypeFull Name
1ABA2Mod. Amino AcidALPHA-AMINOBUTYRIC ACID
2AUX2Mod. Amino Acid4-METHYL-4-[8-QUINOLINIUM-4-ENE]-4,N-METHYL-THREONINE
3DAL2Mod. Amino AcidD-ALANINE
4MLE8Mod. Amino AcidN-METHYLLEUCINE
5MVA2Mod. Amino AcidN-METHYLVALINE
6SAR2Mod. Amino AcidSARCOSINE
Biological Unit 1 (6, 9)
No.NameCountTypeFull Name
1ABA1Mod. Amino AcidALPHA-AMINOBUTYRIC ACID
2AUX1Mod. Amino Acid4-METHYL-4-[8-QUINOLINIUM-4-ENE]-4,N-METHYL-THREONINE
3DAL1Mod. Amino AcidD-ALANINE
4MLE4Mod. Amino AcidN-METHYLLEUCINE
5MVA1Mod. Amino AcidN-METHYLVALINE
6SAR1Mod. Amino AcidSARCOSINE
Biological Unit 2 (6, 9)
No.NameCountTypeFull Name
1ABA1Mod. Amino AcidALPHA-AMINOBUTYRIC ACID
2AUX1Mod. Amino Acid4-METHYL-4-[8-QUINOLINIUM-4-ENE]-4,N-METHYL-THREONINE
3DAL1Mod. Amino AcidD-ALANINE
4MLE4Mod. Amino AcidN-METHYLLEUCINE
5MVA1Mod. Amino AcidN-METHYLVALINE
6SAR1Mod. Amino AcidSARCOSINE

(-) Sites  (0, 0)

(no "Site" information available for 5A0E)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5A0E)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5A0E)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5A0E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5A0E)

(-) Exons   (0, 0)

(no "Exon" information available for 5A0E)

(-) 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:165
                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeee..eeeeeeeeee....hhhhhhhhhhhhhh..........eeeee...eeee................................eeee...........eeee...hhhhh....eeeeeeehhhhhhhhhh............eeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a0e A   1 SGNPLVYLDVDANGKPLGRVVLELKADVVPKTAENFRALCTGEKGFGYKGSTFHRVIPSFMCQAGDFTNHNGTGGKSIYGSRFPDENFTLKHVGPGVLSMANAGPNTNGSQFFICTIKTDWLDGKHVVFGHVIEGMDVVKKIESFGSKSGRTSKKIVITDCGQLS 165
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160     


Chain B 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
                 5a0e B   2 GNPLVYLDVDANGKPLGRVVLELKADVVPKTAENFRALCTGEKGFGYKGSTFHRVIPSFMCQAGDFTNHNGTGGKSIYGSRFPDENFTLKHVGPGVLSMANAGPNTNGSQFFICTIKTDWLDGKHVVFGHVIEGMDVVKKIESFGSKSGRTSKKIVITDCGQLS 165
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161    


Chain C from PDB  Type:PROTEIN  Length:11
                                           
               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
                 5a0e C   1 xllvxaglVlA  11
                            ||||||||10 
                            1-DAL||| | 
                             2-MLE|| | 
                              3-MLE| | 
                               4-MVA | 
                                5-AUX| 
                                 6-ABA 
                                  7-SAR
                                   8-MLE
                                    10-MLE


Chain E from PDB  Type:PROTEIN  Length:11
                                           
               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
                 5a0e E   1 xllvxaglVlA  11
                            ||||||||10 
                            |||||||| | 
                            1-DAL||| | 
                             2-MLE|| | 
                              3-MLE| | 
                               4-MVA | 
                                5-AUX| 
                                 6-ABA 
                                  7-SAR
                                   8-MLE
   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 5A0E)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5A0E)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5A0E)

(-) Gene Ontology  (33, 33)

Asymmetric 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 4j5d 4j5e 4o8h 4o8i 4xnc 4zsc 4zsd 5cbt 5cbu 5cbv 5cbw 5ccn 5ccq 5ccr 5ccs

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