Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF POLO-LIKE KINASE 1
 
Authors :  J. Xu, C. Shen, J. Quan, T. Wang
Date :  13 Feb 13  (Deposition) - 24 Jul 13  (Release) - 08 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  First Complex Structure Of Kd And Pbd Domain, Regulator Of Mitosis, Phosphorylated Target Protein, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Xu, C. Shen, T. Wang, J. Quan
Structural Basis For The Inhibition Of Polo-Like Kinase 1
Nat. Struct. Mol. Biol. V. 20 1047 2013
PubMed-ID: 23893132  |  Reference-DOI: 10.1038/NSMB.2623

(-) Compounds

Molecule 1 - POLO-LIKE KINASE
    Chains: A, D
    EC Number: 2.7.11.21
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: ROSETTA (DE3) PLYSS
    Expression System Taxid: 562
    Fragment: KINASE DOMAIN, UNP RESIDUES 18-312
    Gene: PLK1
    Mutation: YES
    Organism Common: LEOPARD DANIO,ZEBRA DANIO,ZEBRA FISH
    Organism Scientific: DANIO RERIO
    Organism Taxid: 7955
    Synonym: UNCHARACTERIZED PROTEIN
 
Molecule 2 - POLO-LIKE KINASE
    Chains: B, E
    EC Number: 2.7.11.21
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETDUET
    Expression System Strain: ROSETTA (DE3) PLYSS
    Expression System Taxid: 562
    Fragment: POLO BOX DOMAIN, UNP RESIDUES 360-595
    Gene: PLK1
    Mutation: YES
    Organism Common: LEOPARD DANIO,ZEBRA DANIO,ZEBRA FISH
    Organism Scientific: DANIO RERIO
    Organism Taxid: 7955
    Synonym: UNCHARACTERIZED PROTEIN
 
Molecule 3 - 205 KDA MICROTUBULE-ASSOCIATED PROTEIN
    Chains: C, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PETDUET
    Expression System Strain: ROSETTA (DE3) PLYSS
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 276-325
    Gene: MAP205, CG1483
    Organism Common: FRUIT FLY
    Organism Scientific: DROSOPHILA MELANOGASTER
    Organism Taxid: 7227

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABC   
Biological Unit 2 (1x):    DEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4J7B)

(-) Sites  (0, 0)

(no "Site" information available for 4J7B)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4J7B)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4J7B)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4J7B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4J7B)

(-) Exons   (0, 0)

(no "Exon" information available for 4J7B)

(-) 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:284
                                                                                                                                                                                                                                                                                                                            
               SCOP domains d4j7ba_ A: automated matches                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeee....eeeeeeeeeeee..eeeeeeee.....eeeeeeee.hhh.hhhhhhhhhhhhhhhhh........eeeeee...eeeeee......hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee........hhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhh.......hhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j7b A  18 PKSAPLKEIPDVLVDPRTMKRYMRGRFLGKGGFAKCYEITDMDTKEVFAGKVVPKSMLLKPHQKEKMSTEIAIHKSLDNPHVVGFHGFFEDDDFVYVVLEICRRRSLLELHKRRKAVTEPEARYFMRQTIQGVQYLHNNRVIHRNLKLGNLFLNDDMDVKIGDFGLATKICGTPNYIAPEVLCKKGHSFEVDIWSLGCILYTLLVGKPPFETSCLKETYIRIKKNEYSVPRHINPVASALIRRMLHADPTLRPSVAELLTDEFFTSGYAPMRLPTSCLTVPPRF 311
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187|      207       217       227       237       247       257       267       277       287       297       307    
                                                                                                                                                                                                   187|                                                                                                                 
                                                                                                                                                                                                    198                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains d4j7bb1 B:363-491 Serine/threonine-protein kinase plk C-terminal domain                                                d4j7bb2 B:492-585 Serine/threonine-protein kinase plk C-terminal domain                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhh........hhhhhhhhhhh....eeeeee.....eeeeee....eeeee....eeee.....eeeee.....eeeee....hhhhhhhhhhhhhhhhhhh....hhhhh....eeeeee...eeeeee....eeeee....eeeeee....eeeee.....eeeeehhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j7b B 363 THLTDMLQQLAVVNAAKPSDRGFIRQEEAEDPACIPVFWISKWVDYSDKYGLGYQLSDNSVGVLFNDSTRLIMCADGDSLQYIDRNSLESYLSVRSYPSALSKKITLLKYFRNYMSEPREGDELTRLPYLRHWFRTKSAIVLHLSNGTVQINFFQDHTKLILCPLMGAVTYINEKREFYTYKMTLIEEFGCCKELASRLRYARNMVEKLMACK 585
                                   372       382       392       402       412       422       432       442       452       462       472      |492       502       512       522       532       542       552       562       572       582   
                                                                                                                                              479|                                                                                               
                                                                                                                                               490                                                                                               


Chain C from PDB  Type:PROTEIN  Length:49
                                                                                 
               SCOP domains ------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------- Pfam domains
         Sec.struct. author .....ee.................hhhhhhhhhhh..ee.......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------- Transcript
                 4j7b C 276 LDDLVAESPRKEFARINMDGIAVPDEREFDIEADMRPHELEQESDTFGA 324
                                   285       295       305       315         


Chain D from PDB  Type:PROTEIN  Length:281
                                                                                                                                                                                                                                                                                                                         
               SCOP domains d4j7bd_ D: automated matches                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eee......eeeeeeeeeee..eeeeeeee.....eeeeeeee.....hhhhhhhhhhhhhhhhh........eeeeee...eeeeee......hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee.......hhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh.........hhhhhhhhhhhh...............hhhhhh.......hhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j7b D  20 SAPLKEIPDVLVDPRTMKRYMRGRFLGKGGFAKCYEITDMDTKEVFAGKVVPKSMLLKPHQKEKMSTEIAIHKSLDNPHVVGFHGFFEDDDFVYVVLEICRRRSLLELHKRRKAVTEPEARYFMRQTIQGVQYLHNNRVIHRNLKLGNLFLNDDMDVKIGDFGLATKIGTPNYIAPEVLCKKGHSFEVDIWSLGCILYTLLVGKPPFETSCLKETYIRIKKNEYSVPRHINPVASALIRRMLHADPTLRPSVAELLTDEFFTSGYAPMRLPTSCLTVPPRF 311
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       200       210       220       230       240       250       260       270       280       290       300       310 
                                                                                                                                                                                                 187|                                                                                                                
                                                                                                                                                                                                  199                                                                                                                


Chain E from PDB  Type:PROTEIN  Length:213
                                                                                                                                                                                                                                                     
               SCOP domains d4j7be1 E:363-491 Serine/threonine-protein kinase plk C-terminal domain                                                d4j7be2 E:492-585 Serine/threonine-protein kinase plk C-terminal domain                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh....eeeeee.....eeeeee....eeeee....eeee.....eeeee.....eeeee....hhhhhhhhhhhhhhhhhhh....hhhhh....eeeeee...eeeeee....eeeee....eeeeee....eeeee.....eeeeehhhhhhhh.hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j7b E 363 THLTDMLQQLAVVNAAKPSDRGFIRQEEAEDPACIPVFWISKWVDYSDKYGLGYQLSDNSVGVLFNDSTRLIMCADGDSLQYIDRNSLESYLSVRSYPSALSKKITLLKYFRNYMSEPREGDELTRLPYLRHWFRTKSAIVLHLSNGTVQINFFQDHTKLILCPLMGAVTYINEKREFYTYKMTLIEEFGCCKELASRLRYARNMVEKLMACK 585
                                   372       382       392       402       412       422       432       442       452       462       472      |492       502       512       522       532       542       552       562       572       582   
                                                                                                                                              479|                                                                                               
                                                                                                                                               490                                                                                               


Chain F from PDB  Type:PROTEIN  Length:49
                                                                                 
               SCOP domains ------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------- Pfam domains
         Sec.struct. author .....ee.................hhhhhhhhhhh..eee......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------- Transcript
                 4j7b F 276 LDDLVAESPRKEFARINMDGIAVPDEREFDIEADMRPHELEQESDTFGA 324
                                   285       295       305       315
   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  (2, 6)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4J7B)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4J7B)

(-) Gene Ontology  (19, 20)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 4j7b)
 
  Sites
(no "Sites" information available for 4j7b)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4j7b)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4j7b
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  MA205_DROME | P23226
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  Q6DRK7_DANRE | Q6DRK7
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  2.7.11.21
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  MA205_DROME | P23226
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  Q6DRK7_DANRE | Q6DRK7
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        Q6DRK7_DANRE | Q6DRK7: 3dbf
UniProtKB/TrEMBL
        Q6DRK7_DANRE | Q6DRK7: 3d5u 3d5v

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4J7B)