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(-) Description

Title :  CRYSTAL STRUCTURE OF RAT CYCLOPHILIN D IN COMPLEX WITH A POTENT NONIMMUNOSUPPRESSIVE INHIBITOR
 
Authors :  M. S. Knapp, R. A. Elling
Date :  06 Jun 14  (Deposition) - 12 Nov 14  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.39
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,E  (1x)
Biol. Unit 2:  B,F  (1x)
Biol. Unit 3:  C,G  (1x)
Biol. Unit 4:  D,H  (1x)
Keywords :  Inhibitor, Complex, Cyclosporin, Isomerase-Isomerase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Fu, M. Tjandra, C. Becker, D. Bednarczyk, M. Capparelli, R. Elling, I. Hanna, R. Fujimoto, M. Furegati, S. Karur, T. Kasprzyk, M. Knapp, K. Leung, X. Li, P. Lu, W. Mergo, C. Miault, S. Ng, D. Parker, Y. Peng, S. Roggo, A. Rivkin, R. L. Simmons, M. Wang, B. Wiedmann, A. H. Weiss, L. Xiao, L. Xie, W. Xu, A. Yifru, S. Yang, B. Zhou, Z. K. Sweeney
Potent Nonimmunosuppressive Cyclophilin Inhibitors With Improved Pharmaceutical Properties And Decreased Transporte Inhibition.
J. Med. Chem. V. 57 8503 2014
PubMed-ID: 25310383  |  Reference-DOI: 10.1021/JM500862R

(-) Compounds

Molecule 1 - PEPTIDYL-PROLYL CIS-TRANS ISOMERASE F, MITOCHONDRIAL
    Chains: A, B, C, D
    EC Number: 5.2.1.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 43-206
    Gene: PPIF
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: PPIASE F,CYCLOPHILIN D,CYPD,CYCLOPHILIN F,ROTAMASE F
 
Molecule 2 - NONIMMUNOSUPPRESSIVE INHIBITOR
    Chains: E, F, G, H
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): A   E   
Biological Unit 2 (1x):  B   F  
Biological Unit 3 (1x):   C   G 
Biological Unit 4 (1x):    D   H

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (9, 42)

Asymmetric Unit (9, 42)
No.NameCountTypeFull Name
133X4Mod. Amino AcidN-METHYL-D-ALANINE
234E4Mod. Amino Acid(3R)-4-[4-(2-METHOXYETHYL)PIPERAZIN-1-YL]-N-METHYL-L-VALINE
3ABA4Mod. Amino AcidALPHA-AMINOBUTYRIC ACID
4BMT4Mod. Amino Acid4-METHYL-4-[(E)-2-BUTENYL]-4,N-METHYL-THREONINE
5DAL4Mod. Amino AcidD-ALANINE
6MLE12Mod. Amino AcidN-METHYLLEUCINE
7MVA4Mod. Amino AcidN-METHYLVALINE
8P6G4Ligand/IonHEXAETHYLENE GLYCOL
9SO42Ligand/IonSULFATE ION
Biological Unit 1 (9, 11)
No.NameCountTypeFull Name
133X1Mod. Amino AcidN-METHYL-D-ALANINE
234E1Mod. Amino Acid(3R)-4-[4-(2-METHOXYETHYL)PIPERAZIN-1-YL]-N-METHYL-L-VALINE
3ABA1Mod. Amino AcidALPHA-AMINOBUTYRIC ACID
4BMT1Mod. Amino Acid4-METHYL-4-[(E)-2-BUTENYL]-4,N-METHYL-THREONINE
5DAL1Mod. Amino AcidD-ALANINE
6MLE3Mod. Amino AcidN-METHYLLEUCINE
7MVA1Mod. Amino AcidN-METHYLVALINE
8P6G1Ligand/IonHEXAETHYLENE GLYCOL
9SO41Ligand/IonSULFATE ION
Biological Unit 2 (9, 11)
No.NameCountTypeFull Name
133X1Mod. Amino AcidN-METHYL-D-ALANINE
234E1Mod. Amino Acid(3R)-4-[4-(2-METHOXYETHYL)PIPERAZIN-1-YL]-N-METHYL-L-VALINE
3ABA1Mod. Amino AcidALPHA-AMINOBUTYRIC ACID
4BMT1Mod. Amino Acid4-METHYL-4-[(E)-2-BUTENYL]-4,N-METHYL-THREONINE
5DAL1Mod. Amino AcidD-ALANINE
6MLE3Mod. Amino AcidN-METHYLLEUCINE
7MVA1Mod. Amino AcidN-METHYLVALINE
8P6G1Ligand/IonHEXAETHYLENE GLYCOL
9SO41Ligand/IonSULFATE ION
Biological Unit 3 (8, 10)
No.NameCountTypeFull Name
133X1Mod. Amino AcidN-METHYL-D-ALANINE
234E1Mod. Amino Acid(3R)-4-[4-(2-METHOXYETHYL)PIPERAZIN-1-YL]-N-METHYL-L-VALINE
3ABA1Mod. Amino AcidALPHA-AMINOBUTYRIC ACID
4BMT1Mod. Amino Acid4-METHYL-4-[(E)-2-BUTENYL]-4,N-METHYL-THREONINE
5DAL1Mod. Amino AcidD-ALANINE
6MLE3Mod. Amino AcidN-METHYLLEUCINE
7MVA1Mod. Amino AcidN-METHYLVALINE
8P6G1Ligand/IonHEXAETHYLENE GLYCOL
9SO4-1Ligand/IonSULFATE ION
Biological Unit 4 (8, 10)
No.NameCountTypeFull Name
133X1Mod. Amino AcidN-METHYL-D-ALANINE
234E1Mod. Amino Acid(3R)-4-[4-(2-METHOXYETHYL)PIPERAZIN-1-YL]-N-METHYL-L-VALINE
3ABA1Mod. Amino AcidALPHA-AMINOBUTYRIC ACID
4BMT1Mod. Amino Acid4-METHYL-4-[(E)-2-BUTENYL]-4,N-METHYL-THREONINE
5DAL1Mod. Amino AcidD-ALANINE
6MLE3Mod. Amino AcidN-METHYLLEUCINE
7MVA1Mod. Amino AcidN-METHYLVALINE
8P6G1Ligand/IonHEXAETHYLENE GLYCOL
9SO4-1Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREVAL A:93 , GLY A:94 , PRO A:95 , HIS A:131 , LYS B:44 , PHE B:46 , ILE B:78binding site for residue P6G A 201
02AC2SOFTWARELYS A:148 , LYS C:148binding site for residue SO4 A 202
03AC3SOFTWAREPHE A:46 , ILE A:78 , VAL B:93 , GLY B:94 , PRO B:95 , HIS B:131 , HOH B:306 , HOH B:375binding site for residue P6G B 201
04AC4SOFTWARESER B:147 , LYS B:148 , HOH B:318binding site for residue SO4 B 202
05AC5SOFTWAREVAL C:93 , GLY C:94 , PRO C:95 , HIS C:131 , PHE D:46 , SER D:77 , ILE D:78 , GLY D:80binding site for residue P6G C 201
06AC6SOFTWAREPHE C:46 , ILE C:78 , VAL D:93 , GLY D:94 , PRO D:95 , HIS D:131binding site for residue P6G D 201
07AC7SOFTWAREARG A:55 , PHE A:60 , MET A:61 , GLN A:63 , GLY A:72 , THR A:73 , ALA A:101 , ASN A:102 , ALA A:103 , GLN A:111 , PHE A:113 , TRP A:121 , HIS A:126 , ALA C:59 , ILE C:117 , TRP C:121 , HOH E:102 , HOH E:103 , HOH E:104 , HOH E:105 , HOH E:106 , MLE G:2binding site for nonimmunosuppressive inhibitor chain E
08AC8SOFTWAREARG B:55 , PHE B:60 , GLN B:63 , GLY B:72 , THR B:73 , ALA B:101 , ASN B:102 , ALA B:103 , GLN B:111 , PHE B:113 , TRP B:121 , HIS B:126 , ALA D:59 , ILE D:117 , TRP D:121 , HOH F:101 , HOH F:102 , HOH F:104 , MLE H:2binding site for nonimmunosuppressive inhibitor chain F
09AC9SOFTWAREPRO A:58 , ALA A:59 , ARG C:55 , PHE C:60 , MET C:61 , GLN C:63 , GLY C:72 , THR C:73 , ALA C:101 , ASN C:102 , ALA C:103 , GLN C:111 , PHE C:113 , TRP C:121 , LEU C:122 , HIS C:126 , SER D:144 , SER D:153 , LYS D:154 , DAL E:1 , HOH G:103binding site for nonimmunosuppressive inhibitor chain G
10AD1SOFTWAREPRO B:58 , ALA B:59 , PHE C:145 , LYS C:154 , ARG D:55 , PHE D:60 , MET D:61 , GLN D:63 , GLY D:72 , THR D:73 , ALA D:101 , ASN D:102 , ALA D:103 , GLN D:111 , PHE D:113 , TRP D:121 , HIS D:126 , DAL F:1 , MLE F:2 , HOH H:101 , HOH H:102 , HOH H:103 , HOH H:105binding site for nonimmunosuppressive inhibitor chain H

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4TOT)

(-) 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:164
                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee..eeeeeeeeee....hhhhhhhhhhhhhh............eee...eeee................................eeee...........eeee...hhhhh....eeeeeeehhhhhhhhhhh..........eeeeeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tot A   2 QNPLVYLDVGADGQPLGRVVLELKADVVPKTAENFRALCTGEKGFGYKGSTFHRVIPAFMCQAGDFTNHNGTGGKSIYGSRFPDENFTLKHVGPGVLSMANAGPNTNGSQFFICTIKTDWLDGKHVVFGHVIEGMDVVKKIESFGSKSGKTSKKIVITDCGQLS 165
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161    


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..........eeeeeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tot B   2 QNPLVYLDVGADGQPLGRVVLELKADVVPKTAENFRALCTGEKGFGYKGSTFHRVIPAFMCQAGDFTNHNGTGGKSIYGSRFPDENFTLKHVGPGVLSMANAGPNTNGSQFFICTIKTDWLDGKHVVFGHVIEGMDVVKKIESFGSKSGKTSKKIVITDCGQLS 165
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161    


Chain C from PDB  Type:PROTEIN  Length:164
                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee..eeeeeeeeee....hhhhhhhhhhhhhh............eee...eeee................................eeee...........eeee...hhhhh....eeeeeeehhhhhhhhhhh..........eeeeeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tot C   2 QNPLVYLDVGADGQPLGRVVLELKADVVPKTAENFRALCTGEKGFGYKGSTFHRVIPAFMCQAGDFTNHNGTGGKSIYGSRFPDENFTLKHVGPGVLSMANAGPNTNGSQFFICTIKTDWLDGKHVVFGHVIEGMDVVKKIESFGSKSGKTSKKIVITDCGQLS 165
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161    


Chain D from PDB  Type:PROTEIN  Length:164
                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee..eeeeeeeeee....hhhhhhhhhhhhhh............eee...eeee................................eeee...........eeee...hhhhh....eeeeeeehhhhhhhhhhh..........eeeeeeeeee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4tot D   2 QNPLVYLDVGADGQPLGRVVLELKADVVPKTAENFRALCTGEKGFGYKGSTFHRVIPAFMCQAGDFTNHNGTGGKSIYGSRFPDENFTLKHVGPGVLSMANAGPNTNGSQFFICTIKTDWLDGKHVVFGHVIEGMDVVKKIESFGSKSGKTSKKIVITDCGQLS 165
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161    


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
                 4tot E   1 xxxxxxxxVxA  11
                            ||||||||10 
                            1-DAL||| | 
                             2-MLE|| | 
                              3-MLE| | 
                               4-MVA | 
                                5-BMT| 
                                 6-ABA 
                                  7-33X
                                   8-34E
                                    10-MLE


Chain F 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
                 4tot F   1 xxxxxxxxVxA  11
                            ||||||||10 
                            |||||||| | 
                            1-DAL||| | 
                             2-MLE|| | 
                              3-MLE| | 
                               4-MVA | 
                                5-BMT| 
                                 6-ABA 
                                  7-33X
                                   8-34E


Chain G 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
                 4tot G   1 xxxxxxxxVxA  11
                            ||||||||10 
                            |||||||| | 
                            1-DAL||| | 
                             2-MLE|| | 
                              3-MLE| | 
                               4-MVA | 
                                5-BMT| 
                                 6-ABA 
                                  7-33X
                                   8-34E


Chain H 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
                 4tot H   1 xxxxxxxxVxA  11
                            ||||||||10 
                            |||||||| | 
                            1-DAL||| | 
                             2-MLE|| | 
                              3-MLE| | 
                               4-MVA | 
                                5-BMT| 
                                 6-ABA 
                                  7-33X
                                   8-34E
   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 '|'

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