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(-) Description

Title :  CRYSTAL STRUCTURE OF PLK1 POLO-BOX DOMAIN IN COMPLEX WITH PL-74
 
Authors :  W. C. Lee, J. H. Song, H. Y. Kim
Date :  08 Jul 13  (Deposition) - 11 Dec 13  (Release) - 11 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Polo-Box Domain, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. N. Murugan, M. Ahn, W. C. Lee, H. Y. Kim, J. H. Song, C. Cheong, E. Hwang J. H. Seo, S. Y. Shin, S. H. Choi, J. E. Park, J. K. Bang
Exploring The Binding Nature Of Pyrrolidine Pocket-Dependen Interactions In The Polo-Box Domain Of Polo-Like Kinase 1
Plos One V. 8 80043 2013
PubMed-ID: 24223211  |  Reference-DOI: 10.1371/JOURNAL.PONE.0080043

(-) Compounds

Molecule 1 - SERINE/THREONINE-PROTEIN KINASE PLK1
    Chains: A, C
    EC Number: 2.7.11.21
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: POLO-BOX DOMAIN, UNP RESIDUES 371-601
    Gene: PLK1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: POLO-LIKE KINASE 1, PLK-1, SERINE/THREONINE-PROTEIN KINASE 13, STPK13
 
Molecule 2 - PL-74
    Chains: B, D
    Engineered: YES
    Other Details: SOLID PHASE SYNTHESIS
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 12)

Asymmetric Unit (7, 12)
No.NameCountTypeFull Name
15PV1Ligand/Ion5-PHENYLVALERIC ACID
2ACE2Mod. Amino AcidACETYL GROUP
3GOL2Ligand/IonGLYCEROL
4LYT1Ligand/IonBUTYLAMINE
5NH22Mod. Amino AcidAMINO GROUP
6SO42Ligand/IonSULFATE ION
7TPO2Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 1 (7, 7)
No.NameCountTypeFull Name
15PV1Ligand/Ion5-PHENYLVALERIC ACID
2ACE1Mod. Amino AcidACETYL GROUP
3GOL1Ligand/IonGLYCEROL
4LYT1Ligand/IonBUTYLAMINE
5NH21Mod. Amino AcidAMINO GROUP
6SO41Ligand/IonSULFATE ION
7TPO1Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 2 (5, 5)
No.NameCountTypeFull Name
15PV-1Ligand/Ion5-PHENYLVALERIC ACID
2ACE1Mod. Amino AcidACETYL GROUP
3GOL1Ligand/IonGLYCEROL
4LYT-1Ligand/IonBUTYLAMINE
5NH21Mod. Amino AcidAMINO GROUP
6SO41Ligand/IonSULFATE ION
7TPO1Mod. Amino AcidPHOSPHOTHREONINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:517 , ARG A:518 , SER A:519 , TYR A:582BINDING SITE FOR RESIDUE SO4 A 701
2AC2SOFTWARETYR A:421 , ARG A:599 , LYT B:102 , TYR C:445 , SER C:450 , TYR C:462 , LEU C:463BINDING SITE FOR RESIDUE 5PV B 101
3AC3SOFTWARETYR A:417 , TYR A:485 , ACE B:0 , 5PV B:101 , THR C:464BINDING SITE FOR RESIDUE LYT B 102
4AC4SOFTWAREPHE A:535 , HIS A:538 , HIS B:3 , SER B:4 , TPO B:5 , HOH B:201BINDING SITE FOR RESIDUE GOL B 103
5AC5SOFTWARETHR C:517 , ARG C:518 , SER C:519 , TYR C:582BINDING SITE FOR RESIDUE SO4 C 701
6AC6SOFTWAREHOH A:875 , TRP C:414 , PHE C:535 , HIS D:3 , SER D:4 , TPO D:5 , HOH D:201BINDING SITE FOR RESIDUE GOL D 301
7AC7SOFTWARELYS A:413 , TRP A:414 , VAL A:415 , ASP A:416 , TYR A:417 , TYR A:485 , HIS A:489 , LEU A:490 , LEU A:491 , ARG A:516 , HIS A:538 , LYS A:540 , HOH A:829 , LYT B:102 , GOL B:103 , HOH B:201 , HOH B:202 , HOH B:203 , HOH B:204 , HOH B:205 , HOH B:206 , HOH B:207 , SER C:466 , HOH C:830 , HOH C:863BINDING SITE FOR CHAIN B OF PL-74
8AC8SOFTWAREGLU A:399 , TYR A:570 , HOH A:837 , LYS C:413 , TRP C:414 , VAL C:415 , ASP C:416 , TYR C:417 , TYR C:485 , HIS C:489 , LEU C:490 , LEU C:491 , ARG C:516 , HIS C:538 , LYS C:540 , HOH C:801 , HOH D:201 , HOH D:202 , HOH D:203 , HOH D:204 , HOH D:205 , HOH D:206 , HOH D:209 , GOL D:301BINDING SITE FOR CHAIN D OF PL-74

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1His C:468 -Pro C:469

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4LKM)

(-) 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:226
                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh........hhhhhhhhhhh....eeeeee.....eeeeee....eeeee....eeee.....eeeee.....eeeee....hhhhhhhhhhhhhhhhhhhhhh...............eeeeee...eeeeee....eeeee.....eeeee....eeeee.....eeeeehhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lkm A 371 DCHLSDMLQQLHSVNASKPSERGLVRQEEAEDPACIPIFWVSKWVDYSDKYGLGYQLCDNSVGVLFNDSTRLILYNDGDSLQYIERDGTESYLTVSSHPNSLMKKITLLKYFRNYMSEHLLKAGANITPREGLPYLRTWFRTRSAIILHLSNGSVQINFFQDHTKLILCPLMAAVTYIDEKRDFRTYRLSLLEEYGCCKELASRLRYARTMVDKLLSSRSASNRLK 601
                                   380       390       400       410       420       430       440       450       460       470       480       490       500 ||    515       525       535       545       555       565       575       585       595      
                                                                                                                                                             502|                                                                                             
                                                                                                                                                              508                                                                                             


Chain B from PDB  Type:PROTEIN  Length:8
                                        
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ..ee.... Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                 4lkm B   0 xPLHStMx   7
                            |    | |
                            0-ACE| |
                                 5-TPO
                                   7-NH2


Chain C from PDB  Type:PROTEIN  Length:216
                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh........hhhhhhhhhhh....eeeeee.....eeeeee....eeeee....eeee.....eeeee.....eeeee.hhh...hhhhhhhhhhhhhhhhhhh............eeeeee...eeeeee....eeeee.....eeeee....eeeee.....eeeeehhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4lkm C 371 DCHLSDMLQQLHSVNASKPSERGLVRQEEAEDPACIPIFWVSKWVDYSDKYGLGYQLCDNSVGVLFNDSTRLILYNDGDSLQYIERDGTESYLTVSSHPNSLMKKITLLKYFRNYMSEHLLKAGANIARLPYLRTWFRTRSAIILHLSNGSVQINFFQDHTKLILCPLMAAVTYIDEKRDFRTYRLSLLEEYGCCKELASRLRYARTMVDKLLSSR 594
                                   380       390       400       410       420       430       440       450       460       470       480       490      |508       518       528       538       548       558       568       578       588      
                                                                                                                                                        497|                                                                                        
                                                                                                                                                         506                                                                                        


Chain D from PDB  Type:PROTEIN  Length:8
                                        
               SCOP domains -------- SCOP domains
               CATH domains -------- CATH domains
               Pfam domains -------- Pfam domains
         Sec.struct. author ..ee.... Sec.struct. author
                 SAPs(SNPs) -------- SAPs(SNPs)
                    PROSITE -------- PROSITE
                 Transcript -------- Transcript
                 4lkm D   0 xPLHStMx   7
                            |    | |
                            0-ACE| |
                                 5-TPO
                                   7-NH2
   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  (0, 0)

(no "SCOP Domain" information available for 4LKM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (73, 73)

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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 4hco 4hy2 4j52 4j53 4lkl 4o56 4o6w 4o9w 4rcp 4whh 4whk 4whl 4x9r 4x9v 4x9w 5j19 5ta6 5ta8

(-) Related Entries Specified in the PDB File

4lkl