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(-) Description

Title :  CRYSTAL STRUCTURE OF CYCLOPHILIN FROM LEISHMANIA DONOVANI LIGATED WITH CYCLOSPORIN A
 
Authors :  V. Venugopal, D. Dasgupta, A. K. Datta, R. Banerjee
Date :  29 Sep 08  (Deposition) - 11 Nov 08  (Release) - 27 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Isomerase-Immunosuppressant Complex, Cyclophilin-Cyclosporin Complex, Cyclosporin A, Immunosuppressant, Cyclophilin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Venugopal, A. K. Datta, D. Bhattacharyya, D. Dasgupta, R. Banerjee
Structure Of Cyclophilin From Leishmania Donovani Bound To Cyclosporin At 2. 6 A Resolution: Correlation Between Structure And Thermodynamic Data.
Acta Crystallogr. , Sect. D V. 65 1187 2009
PubMed-ID: 19923714  |  Reference-DOI: 10.1107/S0907444909034234
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PEPTIDYL-PROLYL CIS-TRANS ISOMERASE
    Chains: A, B
    EC Number: 5.2.1.8
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE32
    Expression System Strain: M15
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CYP
    Organism Scientific: LEISHMANIA DONOVANI
    Organism Taxid: 5661
    Synonym: PPIASE, ROTAMASE, CYCLOPHILIN
 
Molecule 2 - CYCLOSPORIN A
    Chains: C, D
    Engineered: YES
    Organism Scientific: TOLYPOCLADIUM INFLATUM
    Organism Taxid: 29910
    Synonym: CICLOSPORIN, CICLOSPORINE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

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
2BMT2Mod. Amino Acid4-METHYL-4-[(E)-2-BUTENYL]-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
2BMT1Mod. Amino Acid4-METHYL-4-[(E)-2-BUTENYL]-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
2BMT1Mod. Amino Acid4-METHYL-4-[(E)-2-BUTENYL]-4,N-METHYL-THREONINE
3DAL1Mod. Amino AcidD-ALANINE
4MLE4Mod. Amino AcidN-METHYLLEUCINE
5MVA1Mod. Amino AcidN-METHYLVALINE
6SAR1Mod. Amino AcidSARCOSINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:78 , PHE A:83 , GLN A:86 , GLY A:95 , ALA A:123 , ASN A:124 , GLN A:133 , TRP A:143 , HIS A:148 , PRO B:127 , TRP B:143 , ARG B:147 , HOH C:2001 , MLE D:3 , BMT D:5 , MLE D:10 , ALA D:11BINDING SITE FOR CHAIN C OF CYCLOSPORIN A
2AC2SOFTWAREPRO A:127 , TRP A:143 , ARG A:147 , ARG B:78 , PHE B:83 , GLN B:86 , GLY B:95 , ALA B:123 , ASN B:124 , GLN B:133 , PHE B:135 , TRP B:143 , HIS B:148 , MLE C:3 , BMT C:5 , MLE C:10 , ALA C:11BINDING SITE FOR CHAIN D OF CYCLOSPORIN A

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3EOV)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3EOV)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3EOV)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3EOV)

(-) Exons   (0, 0)

(no "Exon" information available for 3EOV)

(-) 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:166
 aligned with Q9U9R3_LEIDO | Q9U9R3 from UniProtKB/TrEMBL  Length:187

    Alignment length:166
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181      
         Q9U9R3_LEIDO    22 EPEVTAKVYFDVMIDSEPLGRITIGLFGKDAPLTTENFRQLCTGEHGFGYKDSIFHRVIQNFMIQGGDFTNFDGTGGKSIYGEKFADENLNVKHFVGALSMANAGPNTNGSQFFITTAPTPWLDGRHVVFGKVLDGMDVVLRIEKTKTNSHDRPVKPVKIVASGEL 187
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeeee..eeeeeeeeee....hhhhhhhhhhhhhh............eee...eeee...............................eeee...........eeee...hhhhh....eeeeeeehhhhhhhhh....hhhhh....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3eov A  22 EPEVTAKVYFDVMIDSEPLGRITIGLFGKDAPLTTENFRQLCTGEHGFGYKDSIFHRVIQNFMIQGGDFTNFDGTGGKSIYGEKFADENLNVKHFVGALSMANAGPNTNGSQFFITTAPTPWLDGRHVVFGKVLDGMDVVLRIEKTKTNSHDRPVKPVKIVASGEL 187
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181      


Chain B from PDB  Type:PROTEIN  Length:166
 aligned with Q9U9R3_LEIDO | Q9U9R3 from UniProtKB/TrEMBL  Length:187

    Alignment length:166
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181      
         Q9U9R3_LEIDO    22 EPEVTAKVYFDVMIDSEPLGRITIGLFGKDAPLTTENFRQLCTGEHGFGYKDSIFHRVIQNFMIQGGDFTNFDGTGGKSIYGEKFADENLNVKHFVGALSMANAGPNTNGSQFFITTAPTPWLDGRHVVFGKVLDGMDVVLRIEKTKTNSHDRPVKPVKIVASGEL 187
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeeee....eeeeeeeee....hhhhhhhhhhhhhh............eee...eeee...............................eeee...........eeee...hhhhh....eeeeeeehhhhhhhhh....hhhhh.....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3eov B  22 EPEVTAKVYFDVMIDSEPLGRITIGLFGKDAPLTTENFRQLCTGEHGFGYKDSIFHRVIQNFMIQGGDFTNFDGTGGKSIYGEKFADENLNVKHFVGALSMANAGPNTNGSQFFITTAPTPWLDGRHVVFGKVLDGMDVVLRIEKTKTNSHDRPVKPVKIVASGEL 187
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181      


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
                 3eov C   1 xxxxxxxxVxA  11
                            ||||||||10 
                            1-DAL||| | 
                             2-MLE|| | 
                              3-MLE| | 
                               4-MVA | 
                                5-BMT| 
                                 6-ABA 
                                  7-SAR
                                   8-MLE
                                    10-MLE


Chain D 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
                 3eov D   1 xxxxxxxxVxA  11
                            ||||||||10 
                            |||||||| | 
                            1-DAL||| | 
                             2-MLE|| | 
                              3-MLE| | 
                               4-MVA | 
                                5-BMT| 
                                 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 3EOV)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3EOV)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3EOV)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q9U9R3_LEIDO | Q9U9R3)
molecular function
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0003755    peptidyl-prolyl cis-trans isomerase activity    Catalysis of the reaction: peptidyl-proline (omega=180) = peptidyl-proline (omega=0).
biological process
    GO:0006457    protein folding    The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
    GO:0000413    protein peptidyl-prolyl isomerization    The modification of a protein by cis-trans isomerization of a proline residue.

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 Related Entries

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

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        Q9U9R3_LEIDO | Q9U9R3: 2haq 3bt8 4s1e

(-) Related Entries Specified in the PDB File

1bck CRYSTAL STRUCTURE OF HUMAN CYCLOPHILIN A COMPLEXED WITH CYCLOSPORIN C
1c5f CRYSTAL STRUCTURE OF THE CYCLOPHILIN-LIKE DOMAIN FROM BRUGIA MALAYI COMPLEXED WITH CYCLOSPORIN A
1csa SOLUTION STRUCTURE OF E.COLI CYCLOPHILIN (F112W) COMPLEXED WITH CYCLOSPORIN A
1cwa CRYSTAL STRUCTURE OF HUMAN CYCLOPHILIN A COMPLEXED WITH CYCLOSPORIN A
1cwb CRYSTAL STRUCTURE OF HUMAN CYCLOPHILIN A COMPLEXED WITH MODIFIED CYCLOSPORIN A AT POSITION 5
1cwc CRYSTAL STRUCTURE OF HUMAN CYCLOPHILIN A COMPLEXED WITH MODIFIED CYCLOSPORIN A AT POSITION 8
1cwf CRYSTAL STRUCTURE OF HUMAN CYCLOPHILIN A COMPLEXED WITH CYCLOSPORIN D
1cwh CRYSTAL STRUCTURE OF HUMAN CYCLOPHILIN A COMPLEXED WITH CYCLOSPORIN A MODIFIED AT POSITION 7
1cwi CRYSTAL STRUCTURE OF HUMAN CYCLOPHILIN A COMPLEXED WITH MODIFIED CYCLOSPORIN D AT POSITION 7
1cwj CRYSTAL STRUCTURE OF HUMAN CYCLOPHILIN A COMPLEXED WITH MODIFIED CYCLOSPORIN D AT POSITIONS 5 AND 7.
1cwk CRYSTAL STRUCTURE OF HUMAN CYCLOPHILIN A COMPLEXED WITH MODIFIED CYCLOSPORIN D AT POSITIONS 5 AND 7.
1cwl CRYSTAL STRUCTURE OF HUMAN CYCLOPHILIN A COMPLEXED WITH MODIFIED CYCLOSPORIN A AT POSITION 8
1cwm CRYSTAL STRUCTURE OF HUMAN CYCLOPHILIN A COMPLEXED WITH MODIFIED CYCLOSPORIN A AT POSITION 8
1cwo CRYSTAL STRUCTURE OF HUMAN CYCLOPHILIN A COMPLEXED WITH NODIFIED CYCLOSPORIN C AT POSITIONS 1, AND 9
1cya SOLUTION STRUCTURE OF HUMAN CYCLOPHILIN COMPLEXED WIYH CYCLOSPORIN A
1cyb SOLUTION STRUCTURE OF HUMAN CYCLOPHILIN COMPLEXED WITH CYCLOSPORIN A
1cyn CRYSTAL STRUCTURE OF HUMAN CYCLOPHILIN B COMPLEXED WITH MODIFIED CYCLOSPORIN A
1ikf CRYSTAL STRUCTURE OF CTCLOSPORIN-FAB COMPLEX
1m63 CRYSTAL STRUCTURE OF CALCINEURIN-CYCLOPHILIN-CYCLOSPORIN COMPLEX
1mf8 CRYSTAL STRUCTURE OF HUMAN CALCINEURIN COMPLEXED WITH HUMAN CYCLOPHILIN AND CYCLOSPORIN A
1mik CRYSTAL STRUCTURE OF HUMAN CYCLOPHILIN A COMPLEXED WITH MODIFIED CYCLOSPORIN A AT POSITION 6
1qng CRYSTAL STRUCTURE OF PLASMODIUM FALCIPARUM CYCLOPHILIN COMPLEXED WITH CYCLOSPORIN A
1qnh CRYSTAL STRUCTURE OF PLASMODIUM FALCIPARUM CYCLOPHILIN (DOUBLE MUTANT) COMPLEXED WITH CYCLOSPORIN A
1xq7 CRYSTAL STRUCTURE OF TRYPANOSOMA CRUZI CYCLOPHILIN COMPLEXED WITH CYCLOSPORIN A
2esl CRYSTAL STRUCTURE OF HUMAN CYCLOPHILIN C COMPLEXED WITH CYCLOSPORIN A
2haq CRYSTAL STRUCTURE OF NATIVE CYCLOPHILIN FROM LEISHMANIA DONOVANI AT 1.97 A RESOLUTION
2oju CRYSTAL STRUCTURE OF HUMAN CYCLOPHILIN J COMPLEXED WITH CYCLOSPORIN A
2poy CRYSTAL STRUCTURE OF CRYPTOSPORIDIUM PARVUM IOWA II CYCLOPHILIN A COMPLEXED WITH CYCLOSPORIN A
2rma CRYSTAL STRUCTURE OF HUMAN CYCLOPHILIN A COMPLEXED WITH CYCLOSPORIN A
2rmb CRYSTAL STRUCTURE OF HUMAN CYCLOPHILIN A COMPLEXED WITH MODIFIED CYCLOSPORIN A AT POSITION 5
2rmc CRYSTAL STRUCTURE OF MURINE CYCLOPHILIN C COMPLEXED WITH CYCLOSPORIN A
2wfj CRYSTAL STRUCTURE OF THE PPIASE DOMAIN OF HUMAN CYCLOPHILIN G COMPLEXED WITH CYCLOSPORIN A
2x2c CRYSTAL STRUCTURE OF HUMAN ACETYL-CYPA COMPLEXED WITH CYCLOSPORINE A
2x7k CRYSTAL STRUCTURE OF PPIL1 COMPLEXED WITH CYCLOSPORINE A
2z6w CRYSTAL STRUCTURE OF HUMAN CYCLOPHILIN D IN COMPLEX WITH CYCLOSPORIN A
3bo7 CRYSTAL STRUCTURE OF CYCLOSPHILIN A FROM TOXOPLASMA GONDII COMPLEXED WIT CYCLOSPORIN A
3cys SOLUTION STRUCTURE OF THE HUMAN CYCLOSPORIN A COMPLEXED WITH CYCLOSPORIN A