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(-) Description

Title :  HUMAN CYCLOPHILIN D COMPLEXED WITH DIMETHYLFORMAMIDE
 
Authors :  L. Colliandre, H. Ahmed-Belkacem, Y. Bessin, J. M. Pawlotsky, J. F. Gui
Date :  31 Mar 11  (Deposition) - 21 Mar 12  (Release) - 19 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  0.97
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta Barrel, Prolyl Cis/Trans Isomerase, Mitochondria, Inhibitor, Isomerase-Isomerase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Ahmed-Belkacem, L. Colliandre, N. Ahnou, Q. Nevers, M. Gelin, Y. Bessin, R. Brillet, O. Cala, D. Douguet, W. Bourguet, I. Krimm, J. M. Pawlotsky, J. F. Guichou
Fragment-Based Discovery Of A New Family Of Non-Peptidic Small-Molecule Cyclophilin Inhibitors With Potent Antiviral Activities.
Nat Commun V. 7 12777 2016
PubMed-ID: 27652979  |  Reference-DOI: 10.1038/NCOMMS12777

(-) Compounds

Molecule 1 - PEPTIDYL-PROLYL CIS-TRANS ISOMERASE F, MITOCHONDRIAL
    ChainsA
    EC Number5.2.1.8
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentUNP RESIDUES 43-207
    GenePPIF, CYP3
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPPIASE F, CYCLOPHILIN F, ROTAMASE F

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2DMF1Ligand/IonDIMETHYLFORMAMIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:97 , MET A:103 , GLN A:105 , ALA A:143 , ASN A:144 , PHE A:155 , HIS A:168 , HOH A:517 , HOH A:549BINDING SITE FOR RESIDUE DMF A 1
2AC2SOFTWAREARG A:61 , HOH A:555 , HOH A:556 , HOH A:558BINDING SITE FOR RESIDUE CL A 208

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CSA_PPIASE_2PS50072 Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile.PPIF_HUMAN49-205  1A:49-205
2CSA_PPIASE_1PS00170 Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature.PPIF_HUMAN90-107  1A:90-107

(-) Exons   (6, 6)

Asymmetric/Biological Unit (6, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000002251741bENSE00001554110chr10:81107234-81107499266PPIF_HUMAN1-65651A:44-6522
1.2ENST000002251742ENSE00000998348chr10:81108832-8110886231PPIF_HUMAN66-76111A:66-7611
1.3aENST000002251743aENSE00000710825chr10:81109421-8110950989PPIF_HUMAN76-105301A:76-10530
1.4aENST000002251744aENSE00000429803chr10:81111243-8111133997PPIF_HUMAN106-138331A:106-13833
1.5ENST000002251745ENSE00000710835chr10:81112073-8111214876PPIF_HUMAN138-163261A:138-16326
1.6cENST000002251746cENSE00001136191chr10:81113463-811150931631PPIF_HUMAN163-207451A:163-20745

(-) 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:164
 aligned with PPIF_HUMAN | P30405 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:164
                                    53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203    
           PPIF_HUMAN    44 GNPLVYLDVDANGKPLGRVVLELKADVVPKTAENFRALCTGEKGFGYKGSTFHRVIPSFMCQAGDFTNHNGTGGKSIYGSRFPDENFTLKHVGPGVLSMANAGPNTNGSQFFICTIKTDWLDGKHVVFGHVKEGMDVVKKIESFGSKSGRTSKKIVITDCGQLS 207
               SCOP domains d3rcga_ A: Mitochondrial peptidyl-prolyl cis-trans isomerase, cyclophilin F                                                                                          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 (1) -----CSA_PPIASE_2  PDB: A:49-205 UniProt: 49-205                                                                                                                  -- PROSITE (1)
                PROSITE (2) ----------------------------------------------CSA_PPIASE_1      ---------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.1b  PDB: A:44-6Exon 1.2   -----------------------------Exon 1.4a  PDB: A:106-138        ------------------------Exon 1.6c  PDB: A:163-207 UniProt: 163-207    Transcript 1 (1)
           Transcript 1 (2) --------------------------------Exon 1.3a  PDB: A:76-105      --------------------------------Exon 1.5  PDB: A:138-163  -------------------------------------------- Transcript 1 (2)
                 3rcg A  44 GNPLVYLDVDANGKPLGRVVLELKADVVPKTAENFRALCTGEKGFGYKGSTFHRVIPSFMCQAGDFTNHNGTGGKSIYGSRFPDENFTLKHVGPGVLSMANAGPNTNGSQFFICTIKTDWLDGKHVVFGHVIEGMDVVKKIESFGSKSGRTSKKIVITDCGQLS 207
                                    53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203    

   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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (33, 33)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PPIF_HUMAN | P30405)
molecular function
    GO:0016018    cyclosporin A binding    Interacting selectively and non-covalently with cyclosporin A, a cyclic undecapeptide that contains several N-methylated and unusual amino acids.
    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:0042277    peptide binding    Interacting selectively and non-covalently with peptides, any of a group of organic compounds comprising two or more amino acids linked by peptide bonds.
    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).
biological process
    GO:0008637    apoptotic mitochondrial changes    The morphological and physiological alterations undergone by mitochondria during apoptosis.
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0071243    cellular response to arsenic-containing substance    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an arsenic stimulus from compounds containing arsenic, including arsenates, arsenites, and arsenides.
    GO:0071277    cellular response to calcium ion    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a calcium ion stimulus.
    GO:0070301    cellular response to hydrogen peroxide    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hydrogen peroxide (H2O2) stimulus.
    GO:0070266    necroptotic process    A programmed necrotic cell death process which begins when a cell receives a signal (e.g. a ligand binding to a death receptor or to a Toll-like receptor), and proceeds through a series of biochemical events (signaling pathways), characterized by activation of receptor-interacting serine/threonine-protein kinase 1 and/or 3 (RIPK1/3, also called RIP1/3) and by critical dependence on mixed lineage kinase domain-like (MLKL), and which typically lead to common morphological features of necrotic cell death. The process ends when the cell has died. The process is divided into a signaling phase, and an execution phase, which is triggered by the former.
    GO:0032780    negative regulation of ATPase activity    Any process that stops or reduces the rate of ATP hydrolysis by an ATPase.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:2001243    negative regulation of intrinsic apoptotic signaling pathway    Any process that stops, prevents or reduces the frequency, rate or extent of intrinsic apoptotic signaling pathway.
    GO:0090324    negative regulation of oxidative phosphorylation    Any process that decreases the frequency, rate or extent of the chemical reactions and pathways resulting in the phosphorylation of ADP to ATP that accompanies the oxidation of a metabolite through the operation of the respiratory chain. Oxidation of compounds establishes a proton gradient across the membrane, providing the energy for ATP synthesis.
    GO:2000276    negative regulation of oxidative phosphorylation uncoupler activity    Any process that stops, prevents or reduces the frequency, rate or extent of oxidative phosphorylation uncoupler activity.
    GO:0090201    negative regulation of release of cytochrome c from mitochondria    Any process that decreases the rate, frequency or extent of release of cytochrome c from mitochondria, the process in which cytochrome c is enabled to move from the mitochondrial intermembrane space into the cytosol, which is an early step in apoptosis and leads to caspase activation.
    GO:0090200    positive regulation of release of cytochrome c from mitochondria    Any process that increases the rate, frequency or extent of release of cytochrome c from mitochondria, the process in which cytochrome c is enabled to move from the mitochondrial intermembrane space into the cytosol, which is an early step in apoptosis and leads to caspase activation.
    GO:0012501    programmed cell death    A process which begins when a cell receives an internal or external signal and activates a series of biochemical events (signaling pathway). The process ends with the death of the cell.
    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.
    GO:0042981    regulation of apoptotic process    Any process that modulates the occurrence or rate of cell death by apoptotic process.
    GO:0046902    regulation of mitochondrial membrane permeability    Any process that modulates the frequency, rate or extent of the passage or uptake of molecules by the mitochondrial membrane.
    GO:1902445    regulation of mitochondrial membrane permeability involved in programmed necrotic cell death    Any regulation of mitochondrial membrane permeability that is involved in programmed necrotic cell death.
    GO:0010939    regulation of necrotic cell death    Any process that modulates the rate, frequency or extent of necrotic cell death. Necrotic cell death is a cell death process that is morphologically characterized by a gain in cell volume (oncosis), swelling of organelles, plasma membrane rupture and subsequent loss of intracellular contents.
    GO:0010849    regulation of proton-transporting ATPase activity, rotational mechanism    Any process that modulates the rate of ATP hydrolysis by an ATPase. Catalysis of the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: ATP + H2O + H+(in) = ADP + phosphate + H+(out), by a rotational mechanism.
    GO:0002931    response to ischemia    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a inadequate blood supply.
    GO:0006979    response to oxidative stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
cellular component
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005743    mitochondrial inner membrane    The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
    GO:0005759    mitochondrial matrix    The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
    GO:0005753    mitochondrial proton-transporting ATP synthase complex    A proton-transporting ATP synthase complex found in the mitochondrial membrane.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PPIF_HUMAN | P304052bit 2biu 2z6w 3qyu 3r49 3r4g 3r54 3r56 3r57 3r59 3rcf 3rci 3rck 3rcl 3rd9 3rda 3rdb 3rdc 4j58 4j59 4j5a 4j5b 4j5c 4j5d 4j5e 4o8h 4o8i 4xnc 4zsc 4zsd 5a0e 5cbt 5cbu 5cbv 5cbw 5ccn 5ccq 5ccr 5ccs

(-) Related Entries Specified in the PDB File

3r49 3r4g 3r54 3r56 3r57 3r59 3rcf 3rci 3rck 3rcl 3rd9 3rda 3rdb 3rdc 3rdd