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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN PIM1 IN COMPLEX WITH FLUORINATED RUTHENIUM PYRIDOCARBAZOLE
 
Authors :  J. Maksimoska, E. Meggers
Date :  10 Jan 07  (Deposition) - 10 Apr 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  X
Keywords :  Transferase, Pim1, Kinase, Atp-Binding, Phosphorylation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Pagano, J. Maksimoska, H. Bregman, D. S. Williams, R. D. Webster, F. Xue, E. Meggers
Ruthenium Half-Sandwich Complexes As Protein Kinase Inhibitors: Derivatization Of The Pyridocarbazole Pharmacophore Ligand.
Org. Biomol. Chem. V. 5 1218 2007
PubMed-ID: 17406720  |  Reference-DOI: 10.1039/B700433H
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTO-ONCOGENE SERINE/THREONINE-PROTEIN KINASE PIM-1
    ChainsX
    EC Number2.7.11.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPLIC-SGC1
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    GenePIM1
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit X

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric/Biological Unit (4, 6)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2EDO3Ligand/Ion1,2-ETHANEDIOL
3EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
4JM11Ligand/IonFLOURINATED PYRIDOCARBAZOLE CYCLOPENTADIENYL RU(CO)COMPLEX

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL X:69 , GLU X:70 , ARG X:73 , THR X:196 , EDO X:1002 , HOH X:2794BINDING SITE FOR RESIDUE CL X 1001
2AC2SOFTWARELEU X:44 , GLY X:45 , PHE X:49 , VAL X:52 , ALA X:65 , LYS X:67 , ILE X:104 , LEU X:120 , GLU X:121 , ARG X:122 , PRO X:123 , GLU X:171 , LEU X:174 , ILE X:185 , ASP X:186BINDING SITE FOR RESIDUE JM1 X 1000
3AC3SOFTWAREGLY X:47 , GLY X:48 , VAL X:69 , ARG X:73 , CL X:1001BINDING SITE FOR RESIDUE EDO X 1002
4AC4SOFTWARELEU X:34 , GLU X:35 , VAL X:40 , ILE X:66 , HIS X:68BINDING SITE FOR RESIDUE EDO X 1003
5AC5SOFTWAREGLN X:257 , ARG X:258 , ASN X:286 , HOH X:2850BINDING SITE FOR RESIDUE EDO X 1004
6AC6SOFTWAREGLY X:48 , PHE X:49 , LYS X:67 , VAL X:69 , PRO X:87 , GLU X:89 , ASP X:167 , ASP X:186 , GLY X:188 , SER X:189 , ASP X:202 , HOH X:2709 , HOH X:2807BINDING SITE FOR RESIDUE EPE X 2691

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2OI4)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu X:124 -Pro X:125

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 4)

Asymmetric/Biological Unit (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_041004Y144HPIM1_HUMANUnclassified  ---XY53H
2UniProtVAR_041005E215QPIM1_HUMANPolymorphism  ---XE124Q
3UniProtVAR_041006E226KPIM1_HUMANPolymorphism  ---XE135K
4UniProtVAR_041007E233DPIM1_HUMANPolymorphism  ---XE142D

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.PIM1_HUMAN135-158  1X:44-67
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.PIM1_HUMAN254-266  1X:163-175

(-) Exons   (0, 0)

(no "Exon" information available for 2OI4)

(-) 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 X from PDB  Type:PROTEIN  Length:275
 aligned with PIM1_HUMAN | P11309 from UniProtKB/Swiss-Prot  Length:404

    Alignment length:275
                                   132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392     
           PIM1_HUMAN   123 EPLESQYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRISDWGELPNGTRVPMEVVLLKKVSSGFSGVIRLLDWFERPDSFVLILERPEPVQDLFDFITERGALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILIDLNRGELKLIDFGSGALLKDTVYTDFDGTRVYSPPEWIRYHRYHGRSAAVWSLGILLYDMVCGDIPFEHDEEIIRGQVFFRQRVSSECQHLIRWCLALRPSDRPTFEEIQNHPWMQDVLLPQETAEIHLHS 397
               SCOP domains d2oi4x_ X: Proto-oncogene serine/threonine-protein kinase Pim-1                                                                                                                                                                                                                     SCOP domains
               CATH domains 2oi4X01 X:32-124 Phosphorylase Kinase; domain 1                                              2oi4X02 X:125-306 Transferase(Phosphotransferase) domain 1                                                                                                                             CATH domains
               Pfam domains ------Pkinase-2oi4X01 X:38-290                                                                                                                                                                                                                                     ---------------- Pfam domains
         Sec.struct. author ......eeeeeeeeee..eeeeeeee.....eeeeeeee.hhh..ee.......eehhhhhhhhhh........eeeeee...eeeeeee....eeehhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eeee....eeee......ee...........hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.....hhhhhhhh........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhh...hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------H----------------------------------------------------------------------Q----------K------D-------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------PROTEIN_KINASE_ATP      -----------------------------------------------------------------------------------------------PROTEIN_KINAS----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2oi4 X  32 EPLESQYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRISDWGELPNGTRVPMEVVLLKKVSSGFSGVIRLLDWFERPDSFVLILERPEPVQDLFDFITERGALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILIDLNRGELKLIDFGSGALLKDTVYTDFDGTRVYSPPEWIRYHRYHGRSAAVWSLGILLYDMVCGDIPFEHDEEIIGGQVFFRQRVSSECQHLIRWCLALRPSDRPTFEEIQNHPWMQDVLLPQETAEIHLHS 306
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301     

   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: PKinase (934)

(-) Gene Ontology  (27, 27)

Asymmetric/Biological Unit(hide GO term definitions)
Chain X   (PIM1_HUMAN | P11309)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0030145    manganese ion binding    Interacting selectively and non-covalently with manganese (Mn) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
    GO:0004674    protein serine/threonine kinase activity    Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
    GO:0043024    ribosomal small subunit binding    Interacting selectively and non-covalently with any part of the small ribosomal subunit.
    GO:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    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:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0030212    hyaluronan metabolic process    The chemical reactions and pathways involving hyaluronan, the naturally occurring anionic form of hyaluronic acid, any member of a group of glycosaminoglycans, the repeat units of which consist of beta-1,4 linked D-glucuronyl-beta-(1,3)-N-acetyl-D-glucosamine.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    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:0043433    negative regulation of sequence-specific DNA binding transcription factor activity    Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0031659    positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle    Any process that activates or increases the frequency, rate or extent of cyclin-dependent protein serine/threonine kinase activity contributing to the G1/S transition of the cell cycle.
    GO:0046777    protein autophosphorylation    The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation).
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0070561    vitamin D receptor signaling pathway    The series of molecular signals generated as a consequence of a vitamin D receptor binding to one of its physiological ligands.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        PIM1_HUMAN | P113091xqz 1xr1 1xws 1yhs 1yi3 1yi4 1ywv 1yxs 1yxt 1yxu 1yxv 1yxx 2bik 2bil 2bzh 2bzi 2bzj 2bzk 2c3i 2j2i 2o3p 2o63 2o64 2o65 2obj 2xix 2xiy 2xiz 2xj0 2xj1 2xj2 3a99 3bgp 3bgq 3bgz 3bwf 3c4e 3cxw 3cy2 3cy3 3dcv 3f2a 3jpv 3jxw 3jy0 3jya 3ma3 3qf9 3r00 3r01 3r02 3r04 3t9i 3uix 3umw 3umx 3vbq 3vbt 3vbv 3vbw 3vbx 3vby 3vc4 3we8 4a7c 4alu 4alv 4alw 4as0 4bzn 4bzo 4dtk 4enx 4eny 4gw8 4i41 4iaa 4jx3 4jx7 4k0y 4k18 4k1b 4ll5 4lm5 4lmu 4mbi 4mbl 4med 4mta 4n6y 4n6z 4n70 4rbl 4rc2 4rc3 4rc4 4rpv 4ty1 4wrs 4wsy 4wt6 4xh6 4xhk 5c1q 5dgz 5dhj 5dia 5dwr 5eol 5iis 5ipj 5kzi 5v82

(-) Related Entries Specified in the PDB File

1yhs CRYSTAL STRUCTURE OF PIM-1 BOUND TO STAUROSPORINE
2bzh CRYSTAL STRUCTURE OF THE HUMAN PIM1 IN COMPLEX WITH A RUTHENIUM ORGANOMETALLIC LIGAND RU1
2bzi CRYSTAL STRUCTURE OF THE HUMAN PIM1 IN COMPLEX WITH A RUTHENIUM ORGANOMETALLIC LIGAND RU2
2bzj CRYSTAL STRUCTURE OF THE HUMAN PIM1 IN COMPLEX WITH A RUTHENIUM ORGANOMETALLIC LIGAND RU3