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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CYCLOPHILN_RING DOMAIN OF HUMAN PEPTIDYLPROLYL ISOMERASE (CYCLOPHILIN)-LIKE 2 ISOFORM B
 
Authors :  J. R. Walker, T. Davis, E. M. Newman, F. Mackenzie, J. Weigelt, M. Sundstrom, C. Arrowsmith, A. Edwards, A. Bochkarev, S. Dhe- Paganon, Structural Genomics Consortium (Sgc)
Date :  02 May 05  (Deposition) - 16 Aug 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Cis-Trans Isomerization, Peptidylprolyl Isomerase, Protein- Folding, Structural Genomics Consortium, Sgc (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. R. Walker, T. Davis, E. M. Newman, F. Mackenzie, J. Weigelt, M. Sundstrom, C. Arrowsmith, A. Edwards, A. Bochkarev, S. Dhe-Paganon, Structural Genomics Consortium (Sgc)
Crystal Structure Of The Human Peptidylprolyl Isomerase-Like 2 Isoform B
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PEPTIDYL-PROLYL CIS-TRANS ISOMERASE LIKE 2
    ChainsA, B
    EC Number5.2.1.8
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET28-LIC
    Expression System StrainBL21 (DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentSEQUENCE DATABANK RESIDUES 20-197
    GenePPIL2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPPIASE, ROTAMASE, CYCLOPHILIN-60, CYCLOPHILIN- LIKE PROTEIN CYP-60, CYCLOPHILIN-RING DOMAIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1BME2Ligand/IonBETA-MERCAPTOETHANOL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1BME1Ligand/IonBETA-MERCAPTOETHANOL
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1BME1Ligand/IonBETA-MERCAPTOETHANOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:327 , ARG A:385 , SER A:386 , CYS A:387 , VAL A:455BINDING SITE FOR RESIDUE BME A 638
2AC2SOFTWAREASN B:327 , PHE B:328 , ARG B:385 , SER B:386 , CYS B:387 , VAL B:455BINDING SITE FOR RESIDUE BME B 639

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:297 -A:304

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1ZKC)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1ZKC)

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CSA_PPIASE_2PS50072 Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile.PPIL2_HUMAN285-433
 
  2A:285-433
B:285-433
2CSA_PPIASE_1PS00170 Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature.PPIL2_HUMAN316-333
 
  2A:316-333
B:316-333
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CSA_PPIASE_2PS50072 Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile.PPIL2_HUMAN285-433
 
  1A:285-433
-
2CSA_PPIASE_1PS00170 Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature.PPIL2_HUMAN316-333
 
  1A:316-333
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CSA_PPIASE_2PS50072 Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile.PPIL2_HUMAN285-433
 
  1-
B:285-433
2CSA_PPIASE_1PS00170 Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature.PPIL2_HUMAN316-333
 
  1-
B:316-333

(-) Exons   (9, 18)

Asymmetric Unit (9, 18)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.7dENST000003988317dENSE00001783855chr22:22020311-22020420110PPIL2_HUMAN1-11110--
1.9aENST000003988319aENSE00000879341chr22:22024202-2202425150PPIL2_HUMAN11-28180--
1.10aENST0000039883110aENSE00001745860chr22:22024855-2202490046PPIL2_HUMAN28-43160--
1.10cENST0000039883110cENSE00001621823chr22:22025286-2202534863PPIL2_HUMAN43-64220--
1.11ENST0000039883111ENSE00001606560chr22:22026619-2202667052PPIL2_HUMAN64-81180--
1.13ENST0000039883113ENSE00001636121chr22:22029353-2202940452PPIL2_HUMAN82-99180--
1.15aENST0000039883115aENSE00002194623chr22:22035588-2203567992PPIL2_HUMAN99-129310--
1.16ENST0000039883116ENSE00001687385chr22:22036726-2203681590PPIL2_HUMAN130-159300--
1.17ENST0000039883117ENSE00001654978chr22:22037471-2203754676PPIL2_HUMAN160-185260--
1.18bENST0000039883118bENSE00001714065chr22:22039042-22039202161PPIL2_HUMAN185-238540--
1.20ENST0000039883120ENSE00001711283chr22:22040772-2204084776PPIL2_HUMAN239-264262A:271-279
B:273-279
9
7
1.21ENST0000039883121ENSE00001668058chr22:22041181-22041287107PPIL2_HUMAN264-299362A:280-299
B:280-299
20
20
1.22ENST0000039883122ENSE00001749741chr22:22041932-2204202190PPIL2_HUMAN300-329302A:300-329
B:300-329
30
30
1.23ENST0000039883123ENSE00001786549chr22:22042362-2204239534PPIL2_HUMAN330-341122A:330-341
B:330-341
12
12
1.24ENST0000039883124ENSE00001668073chr22:22043021-22043138118PPIL2_HUMAN341-380402A:341-380
B:341-380
40
40
1.25ENST0000039883125ENSE00001804654chr22:22048105-2204816157PPIL2_HUMAN380-399202A:380-399
B:380-399
20
20
1.26aENST0000039883126aENSE00001731119chr22:22048882-2204895473PPIL2_HUMAN399-423252A:399-423
B:399-423
25
25
1.26cENST0000039883126cENSE00001608454chr22:22049044-2204910663PPIL2_HUMAN424-444212A:424-444
B:424-444
21
21
1.27bENST0000039883127bENSE00001623901chr22:22049226-22049359134PPIL2_HUMAN445-489452A:445-457
B:445-457
13
13
1.27eENST0000039883127eENSE00001651605chr22:22049683-220507121030PPIL2_HUMAN489-520320--

(-) 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:187
 aligned with PPIL2_HUMAN | Q13356 from UniProtKB/Swiss-Prot  Length:520

    Alignment length:206
                                   261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451      
          PPIL2_HUMAN   252 STAMVPETTHEAAAIDEDVLRYQFVKKKGYVRLHTNKGDLNLELHCDLTPKTCENFIRLCKKHYYDGTIFHRSIRNFVIQGGDPTGTGTGGESYWGKPFKDEFRPNLSHTGRGILSMANSGPNSNRSQFFITFRSCAYLDKKHTIFGRVVGGFDVLTAMENVESDPKTDRPKEEIRIDATTVFVDPYEEADAQIAQERKTQLKVAP 457
               SCOP domains ----------------------------d1zkca1 A:280-457 Peptidyl-prolyl cis-trans isomerase-like 2, Cyclophilin-60, PPI domain                                                                                           SCOP domains
               CATH domains 1zkcA00 A                   :271-457 Cyclophilin                                                                                                                                                               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........-------------------eeeeeee..eeeeeee....hhhhhhhhhhhhhh.......eeeee...eeee................................eeee...........eeee...hhhhh....eeeeeeehhhhhhhhhhh..............eeeeeeee..hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------------------CSA_PPIASE_2  PDB: A:285-433 UniProt: 285-433                                                                                                        ------------------------ PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------CSA_PPIASE_1      ---------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.20    -----------------------------------Exon 1.22  PDB: A:300-329     Exon 1.23   --------------------------------------Exon 1.25           ------------------------Exon 1.26c           Exon 1.27b    Transcript 1 (1)
           Transcript 1 (2) ------------Exon 1.21  PDB: A:280-299           -----------------------------------------Exon 1.24  PDB: A:341-380               ------------------Exon 1.26a  PDB: A:399-42---------------------------------- Transcript 1 (2)
                 1zkc A 271 SSGLVPRGS-------------------GYVRLHTNKGDLNLELHCDLTPKTCENFIRLCKKHYYDGTIFHRSIRNFVIQGGDPTGTGTGGESYWGKPFKDEFRPNLSHTGRGILSMANSGPNSNRSQFFITFRSCAYLDKKHTIFGRVVGGFDVLTAMENVESDPKTDRPKEEIRIDATTVFVDPYEEADAQIAQERKTQLKVAP 457
                                    |-         -       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451      
                                  279                 280                                                                                                                                                                                 

Chain B from PDB  Type:PROTEIN  Length:185
 aligned with PPIL2_HUMAN | Q13356 from UniProtKB/Swiss-Prot  Length:520

    Alignment length:204
                                   263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453    
          PPIL2_HUMAN   254 AMVPETTHEAAAIDEDVLRYQFVKKKGYVRLHTNKGDLNLELHCDLTPKTCENFIRLCKKHYYDGTIFHRSIRNFVIQGGDPTGTGTGGESYWGKPFKDEFRPNLSHTGRGILSMANSGPNSNRSQFFITFRSCAYLDKKHTIFGRVVGGFDVLTAMENVESDPKTDRPKEEIRIDATTVFVDPYEEADAQIAQERKTQLKVAP 457
               SCOP domains d1zkcb_                    B: Peptidyl-prolyl cis-trans isomerase-like 2, Cyclophilin-60, PPI domain                                                                                                         SCOP domains
               CATH domains ------1                   zkcB01 B:279-438 Cyclophilin                                                                                                                                   ------------------- CATH domains
           Pfam domains (1) ---------------------------Pro_isomerase-1zkcB01 B:281-433                                                                                                                          ------------------------ Pfam domains (1)
           Pfam domains (2) ---------------------------Pro_isomerase-1zkcB02 B:281-433                                                                                                                          ------------------------ Pfam domains (2)
         Sec.struct. author .......-------------------eeeeeee..eeeeeee....hhhhhhhhhhhhhh.....eeeeeee...eeee................................eeee...........eeee...hhhhh....eeeeeeehhhhhhhhhh..............eeeeeeeee..hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -------------------------------CSA_PPIASE_2  PDB: B:285-433 UniProt: 285-433                                                                                                        ------------------------ PROSITE (1)
                PROSITE (2) --------------------------------------------------------------CSA_PPIASE_1      ---------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.20  -----------------------------------Exon 1.22  PDB: B:300-329     Exon 1.23   --------------------------------------Exon 1.25           ------------------------Exon 1.26c           Exon 1.27b    Transcript 1 (1)
           Transcript 1 (2) ----------Exon 1.21  PDB: B:280-299           -----------------------------------------Exon 1.24  PDB: B:341-380               ------------------Exon 1.26a  PDB: B:399-42---------------------------------- Transcript 1 (2)
                 1zkc B 273 GLVPRGS-------------------GYVRLHTNKGDLNLELHCDLTPKTCENFIRLCKKHYYDGTIFHRSIRNFVIQGGDPTGTGTGGESYWGKPFKDEFRPNLSHTGRGILSMANSGPNSNRSQFFITFRSCAYLDKKHTIFGRVVGGFDVLTAMENVESDPKTDRPKEEIRIDATTVFVDPYEEADAQIAQERKTQLKVAP 457
                                  |  -         -      |283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453    
                                279                 280                                                                                                                                                                                 

   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  (1, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 2)

Asymmetric Unit

(-) Gene Ontology  (18, 18)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PPIL2_HUMAN | Q13356)
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:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0003755    peptidyl-prolyl cis-trans isomerase activity    Catalysis of the reaction: peptidyl-proline (omega=180) = peptidyl-proline (omega=0).
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0061630    ubiquitin protein ligase activity    Catalysis of the transfer of ubiquitin to a substrate protein via the reaction X-ubiquitin + S -> X + S-ubiquitin, where X is either an E2 or E3 enzyme, the X-ubiquitin linkage is a thioester bond, and the S-ubiquitin linkage is an amide bond: an isopeptide bond between the C-terminal glycine of ubiquitin and the epsilon-amino group of lysine residues in the substrate or, in the linear extension of ubiquitin chains, a peptide bond the between the C-terminal glycine and N-terminal methionine of ubiquitin residues.
    GO:0004842    ubiquitin-protein transferase activity    Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
    GO:0034450    ubiquitin-ubiquitin ligase activity    Isoenergetic transfer of ubiquitin from one protein to an existing ubiquitin chain via the reaction X-ubiquitin + Y-ubiquitin -> Y-ubiquitin-ubiquitin + X, where both the X-ubiquitin and Y-ubiquitin-ubiquitin linkages are thioester bonds between the C-terminal glycine of ubiquitin and a sulfhydryl side group of a cysteine residue.
biological process
    GO:0050900    leukocyte migration    The movement of a leukocyte within or between different tissues and organs of the body.
    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:0072659    protein localization to plasma membrane    A process in which a protein is transported to, or maintained in, a specific location in the plasma membrane.
    GO:0000413    protein peptidyl-prolyl isomerization    The modification of a protein by cis-trans isomerization of a proline residue.
    GO:0000209    protein polyubiquitination    Addition of multiple ubiquitin groups to a protein, forming a ubiquitin chain.
    GO:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.
cellular component
    GO:0005796    Golgi lumen    The volume enclosed by the membranes of any cisterna or subcompartment of the Golgi apparatus, including the cis- and trans-Golgi networks.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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