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(-) Description

Title :  HUMAN PLK1-PBD IN COMPLEX WITH THYMOQUINONE AT THE PHOPHOPEPTIDE BINDING SITE
 
Authors :  Z. Yin, P. H. Rehse
Date :  01 Oct 12  (Deposition) - 10 Oct 12  (Release) - 06 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.75
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  B  (1x)
Biol. Unit 2:  A  (1x)
Keywords :  Kinase, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Yin, Y. Song, P. H. Rehse
Thymoquinone Blocks Pser/Pthr Recognition By Plk1 Polo-Box Domain As A Phosphate Mimic
Acs Chem. Biol. V. 8 303 2013
PubMed-ID: 23135290  |  Reference-DOI: 10.1021/CB3004379

(-) Compounds

Molecule 1 - SERINE/THREONINE-PROTEIN KINASE PLK1
    Chains: B, A
    EC Number: 2.7.11.21
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 367-603
    Gene: PLK1, PLK
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: POLO-LIKE KINASE 1, PLK-1, SERINE/THREONINE-PROTEIN KINASE 13, STPK13

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2IMW1Ligand/Ion2-METHYL-5-(1-METHYLETHYL)CYCLOHEXA-2,5-DIENE-1,4-DIONE
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2IMW-1Ligand/Ion2-METHYL-5-(1-METHYLETHYL)CYCLOHEXA-2,5-DIENE-1,4-DIONE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2IMW1Ligand/Ion2-METHYL-5-(1-METHYLETHYL)CYCLOHEXA-2,5-DIENE-1,4-DIONE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:414 , GLU A:460 , LEU A:490 , IMW A:702BINDING SITE FOR RESIDUE GOL A 701
2AC2SOFTWAREGLU A:460 , LEU A:491 , ALA A:493 , ARG A:507 , HIS A:538 , LYS A:540 , ARG A:557 , GOL A:701 , HOH A:802 , HOH A:805BINDING SITE FOR RESIDUE IMW A 702

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4HCO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HCO)

(-) 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:220
                                                                                                                                                                                                                                                            
               SCOP domains d4hcoa1 A:373-500 Serine/threonine-protein kinase plk C-terminal domain                                                         d4hcoa2 A:501-593 Serine/threonine-protein kinase plk C-terminal domain                      SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh........hhhhhh.........eeeeee.....eeeeee....eeeee....eeee.....eeeee.....eeeee.......hhhhhhhhhhhhhhhhhhh...................eeeeee...eeeeee....eeeee.....eeeee....eeeee.....eeeeehhhhhhhh.hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hco A 373 HLSDMLQQLHSVNASKPSERGLVRQEEAEDPACIPIFWVSKWVDYSDKYGLGYQLCDNSVGVLFNDSTRLILYNDGDSLQYIERDGTESYLTVSSHPNSLMKKITLLKYFRNYMSEHLLKAGANITPREGDLARLPYLRTWFRTRSAIILHLSNGSVQINFFQDHTKLILCPLMAAVTYIDEKRDFRTYRLSLLEEYGCCKELASRLRYARTMVDKLLSS 593
                                   382       392       402       412       422       432       442       452       462       472       482       492       502||     513       523       533       543       553       563       573       583       593
                                                                                                                                                            503|                                                                                        
                                                                                                                                                             505                                                                                        


Chain B from PDB  Type:PROTEIN  Length:220
                                                                                                                                                                                                                                                            
               SCOP domains d4hcob1 B:371-500 Serine/threonine-protein kinase plk C-terminal domain                                                           d4hcob2 B:505-594 Serine/threonine-protein kinase plk C-terminal domain                    SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh.hhhhh...hhhhhhhhhhh....eeeeeee....eeeeee....eeeee....eeee.....eeeee.....eeeee.hhhhhhhhhhhhhhhhhhhhhhhhh................eeeeee...eeeeee....eeeee.....eeeee....eeeee.....eeeeehhhhhhhh.hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hco B 371 DCHLSDMLQQLHSVNASKPSERGLVRQEEAEDPACIPIFWVSKWVDYSDKYGLGYQLCDNSVGVLFNDSTRLILYNDGDSLQYIERDGTESYLTVSSHPNSLMKKITLLKYFRNYMSEHLLKAGANITPRLARLPYLRTWFRTRSAIILHLSNGSVQINFFQDHTKLILCPLMAAVTYIDEKRDFRTYRLSLLEEYGCCKELASRLRYARTMVDKLLSSR 594
                                   380       390       400       410       420       430       440       450       460       470       480       490       500|      514       524       534       544       554       564       574       584       594
                                                                                                                                                           500|                                                                                         
                                                                                                                                                            505
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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, 4)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (72, 72)

Asymmetric Unit(hide GO term definitions)

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  4hco
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  PLK1_HUMAN | P53350
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  2.7.11.21
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 Related Entries

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

UniProtKB/Swiss-Prot
        PLK1_HUMAN | P53350: 1q4k 1q4o 1umw 2ogq 2ojx 2ou7 2owb 2rku 2v5q 2yac 3bzi 3c5l 3fc2 3fvh 3hih 3hik 3kb7 3p2w 3p2z 3p34 3p35 3p36 3p37 3q1i 3rq7 3thb 4a4l 4a4o 4dfw 4e67 4e9c 4e9d 4h5x 4h71 4hab 4hy2 4j52 4j53 4lkl 4lkm 4o56 4o6w 4o9w 4rcp 4whh 4whk 4whl 4x9r 4x9v 4x9w 5j19 5ta6 5ta8

(-) Related Entries Specified in the PDB File

4h5x THE SAME PROTEIN, DIFFERENT LIGAND
4h71 THE SAME PROTEIN, DIFFERENT LIGAND