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(-) Description

Title :  CRYSTAL STRUCTURE OF PIM-1 IN COMPLEX WITH THE FLUORESCENT COMPOUND SKF86002
 
Authors :  L. J. Parker, A. Tanaka, N. Handa, K. Honda, Y. Tomabechi, M. Shirouzu, S
Date :  09 Jul 13  (Deposition) - 12 Feb 14  (Release) - 12 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Co-Crystallization, Skf86002, Fluorescence, Inhibitor Screening, Kinase, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. J. Parker, S. Taruya, K. Tsuganezawa, N. Ogawa, J. Mikuni, K. Honda, T. Tomabechi, N. Handa, M. Shirouzu, S. Yokoyama, A. Tanaka
Kinase Crystal Identification And Atp-Competitive Inhibitor Screening Using The Fluorescent Ligand Skf86002
Acta Crystallogr. , Sect. D V. 70 392 2014
PubMed: search  |  Reference-DOI: 10.1107/S1399004713028654

(-) Compounds

Molecule 1 - SERINE/THREONINE-PROTEIN KINASE PIM-1
    Chains: A
    EC Number: 2.7.11.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PCR2.1-TOPO
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: PROTEIN KINASE DOMAIN, UNP RESODIES 120-404
    Gene: PIM1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PROTO-ONCOGENE SERINE/THREONINE-PROTEIN KINASE PIM-1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2GOL4Ligand/IonGLYCEROL
3SK81Ligand/Ion6-(4-FLUOROPHENYL)-5-(PYRIDIN-4-YL)-2,3-DIHYDROIMIDAZO[2,1-B][1,3]THIAZOLE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:49 , ALA A:65 , GLU A:121 , ARG A:122 , PRO A:123 , LEU A:174 , ASP A:186BINDING SITE FOR RESIDUE SK8 A 401
2AC2SOFTWAREPHE A:130 , ILE A:133 , ASP A:170 , ASP A:234 , GLY A:238 , ASP A:239 , CA A:406 , HOH A:669BINDING SITE FOR RESIDUE GOL A 402
3AC3SOFTWAREHIS A:265 , HIS A:287 , PRO A:288 , HOH A:644BINDING SITE FOR RESIDUE GOL A 403
4AC4SOFTWAREASP A:108 , TRP A:109 , PHE A:110BINDING SITE FOR RESIDUE GOL A 404
5AC5SOFTWAREASP A:167 , LYS A:169 , ASP A:202 , HOH A:673BINDING SITE FOR RESIDUE GOL A 405
6AC6SOFTWAREASP A:170 , TYR A:207 , ILE A:240 , GOL A:402 , HOH A:668 , HOH A:669BINDING SITE FOR RESIDUE CA A 406

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4LL5)

(-) Cis Peptide Bonds  (1, 1)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4LL5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4LL5)

(-) Exons   (0, 0)

(no "Exon" information available for 4LL5)

(-) 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:268
                                                                                                                                                                                                                                                                                                            
               SCOP domains d4ll5a_ A: Proto-oncogene serine/threonine-protein kinase Pim-1                                                                                                                                                                                                              SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ll5 A  34 LESQYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRISDWGETRVPMEVVLLKKVSSGFSGVIRLLDWFERPDSFVLILERPEPVQDLFDFITERGALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILIDLNRGELKLIDFGSGALLKDTVYTDFDGTRVYSPPEWIRYHRYHGRSAAVWSLGILLYDMVCGDIPFEHDEEIIRGQVFFRQRVSSECQHLIRWCLALRPSDRPTFEEIQNHPWMQDVLLPQETAEIHLH 305
                                    43        53        63        73     || 87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297        
                                                                        79|                                                                                                                                                                                                                             
                                                                         84
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  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
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4LL5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4LL5)

(-) Gene Ontology  (27, 27)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Glu A:124 - Pro A:125   [ RasMol ]  
 

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  2.7.11.1
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 Related Entries

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

UniProtKB/Swiss-Prot
        PIM1_HUMAN | P11309: 1xqz 1xr1 1xws 1yhs 1yi3 1yi4 1ywv 1yxs 1yxt 1yxu 1yxv 1yxx 2bik 2bil 2bzh 2bzi 2bzj 2bzk 2c3i 2j2i 2o3p 2o63 2o64 2o65 2obj 2oi4 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 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

4lm5 4lmu 4lud 4lue