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(-) Description

Title :  CRYSTAL STRUCTURE OF THE FK506 BINDING DOMAIN OF PLASMODIUM VIVAX FKBP35
 
Authors :  I. A. Qureshi, H. S. Yoon, J. Lescar
Date :  15 Jun 10  (Deposition) - 27 Apr 11  (Release) - 09 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.42
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Fk506 Binding Domain, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Alag, A. M. Balakrishna, S. Rajan, I. A. Qureshi, J. Shin, J. Lescar, G. Gruber, H. S. Yoon
Structural Insights Into Substrate Binding By Pvfkbp35, A Peptidylprolyl Cis-Trans Isomerase From The Human Malarial Parasite Plasmodium Vivax
Eukaryotic Cell V. 12 627 2013
PubMed-ID: 23435727  |  Reference-DOI: 10.1128/EC.00016-13

(-) Compounds

Molecule 1 - 70 KDA PEPTIDYLPROLYL ISOMERASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PSUMO
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: FK506-BINDING DOMAIN, RESIDUES 1-126
    Organism Scientific: PLASMODIUM VIVAX
    Organism Taxid: 5855

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric/Biological Unit (1, 8)
No.NameCountTypeFull Name
1GOL8Ligand/IonGLYCEROL

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:55 , VAL A:73 , ILE A:74 , TYR A:100 , PHE A:117BINDING SITE FOR RESIDUE GOL A 127
2AC2SOFTWAREGLY A:36 , HIS A:67 , GLU A:126BINDING SITE FOR RESIDUE GOL A 128
3AC3SOFTWAREGLU A:102 , GLY A:111 , ASN A:112 , HOH A:199 , HOH A:463 , GLU B:103BINDING SITE FOR RESIDUE GOL A 129
4AC4SOFTWAREGLN A:70 , GLU A:72 , HOH A:206 , HOH B:153BINDING SITE FOR RESIDUE GOL A 130
5AC5SOFTWARELYS B:35BINDING SITE FOR RESIDUE GOL B 127
6AC6SOFTWAREGLU A:7 , HOH A:373 , ALA B:82 , HOH B:135 , HOH B:297BINDING SITE FOR RESIDUE GOL B 128
7AC7SOFTWAREVAL B:73 , ILE B:74 , TRP B:77 , TYR B:100 , HOH B:409BINDING SITE FOR RESIDUE GOL B 129
8AC8SOFTWAREGLU A:13 , ASP A:14 , GLY A:15 , HOH A:149 , HOH A:162BINDING SITE FOR RESIDUE GOL B 130

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:105 -B:105

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3NI6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3NI6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3NI6)

(-) Exons   (0, 0)

(no "Exon" information available for 3NI6)

(-) 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:124
 aligned with A5K8X6_PLAVS | A5K8X6 from UniProtKB/TrEMBL  Length:302

    Alignment length:124
                                    12        22        32        42        52        62        72        82        92       102       112       122    
         A5K8X6_PLAVS     3 QETLEQVHLTEDGGVVKTILRKGEGGEENAPKKGNEVTVHYVGKLESSGKVFDSSRERNVPFKFHLGQGEVIKGWDICVASMTKNEKCSVRLDSKYGYGEEGCGESIPGNSVLIFEIELISFRE 126
               SCOP domains d3ni6a_ A: automated matches                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee......eeeeeee..............eeeeeeeeee.....eeeehhhhh..eeee......hhhhhhhhhh.....eeeeee.hhhh...............eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ni6 A   3 QETLEQVHLTEDGGVVKTILRKGEGGEENAPKKGNEVTVHYVGKLESSGKVFDSSRERNVPFKFHLGQGEVIKGWDICVASMTKNEKCSVRLDSKYGYGEEGCGESIPGNSVLIFEIELISFRE 126
                                    12        22        32        42        52        62        72        82        92       102       112       122    


Chain B from PDB  Type:PROTEIN  Length:121
 aligned with A5K8X6_PLAVS | A5K8X6 from UniProtKB/TrEMBL  Length:302

    Alignment length:121
                                    15        25        35        45        55        65        75        85        95       105       115       125 
         A5K8X6_PLAVS     6 LEQVHLTEDGGVVKTILRKGEGGEENAPKKGNEVTVHYVGKLESSGKVFDSSRERNVPFKFHLGQGEVIKGWDICVASMTKNEKCSVRLDSKYGYGEEGCGESIPGNSVLIFEIELISFRE 126
               SCOP domains d3ni6b_ B: automated matches                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------FKBP_C-3ni6B01 B:29-122                                                                       ---- Pfam domains (1)
           Pfam domains (2) -----------------------FKBP_C-3ni6B02 B:29-122                                                                       ---- Pfam domains (2)
         Sec.struct. author ..eee......eeeeeee..............eeeeeeeeee.....eeeehhhhh..eeee......hhhhhhhhhh.....eeeeee.hhhh...............eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ni6 B   6 LEQVHLTEDGGVVKTILRKGEGGEENAPKKGNEVTVHYVGKLESSGKVFDSSRERNVPFKFHLGQGEVIKGWDICVASMTKNEKCSVRLDSKYGYGEEGCGESIPGNSVLIFEIELISFRE 126
                                    15        25        35        45        55        65        75        85        95       105       115       125
   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, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3NI6)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: FKBP_C] (58)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (A5K8X6_PLAVS | A5K8X6)
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.
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.

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 Related Entries

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UniProtKB/TrEMBL
        A5K8X6_PLAVS | A5K8X6: 2ki3 3ihz 3pa7 4itz 4j4o 4mgv

(-) Related Entries Specified in the PDB File

2vn1 3ihz