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

(-) Description

Title :  WILMS TUMOR PROTEIN (WT1) ZNF2-4 Q369H IN COMPLEX WITH FORMYLATED DNA
 
Authors :  H. Hashimoto, X. Cheng
Date :  23 Jun 16  (Deposition) - 14 Sep 16  (Release) - 14 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.78
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  Wilms Tumor Protein, Wt1, Zinc Finger, 5-Formyl Cytosine, Transcription-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Hashimoto, X. Zhang, Y. Zheng, G. G. Wilson, X. Cheng
Denys-Drash Syndrome Associated Wt1 Glutamine 369 Mutants Have Altered Sequence-Preferences And Altered Responses To Epigenetic Modifications.
Nucleic Acids Res. V. 44 10165 2016
PubMed-ID: 27596598  |  Reference-DOI: 10.1093/NAR/GKW766

(-) Compounds

Molecule 1 - WILMS TUMOR PROTEIN
    Chains: A, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PXC1305
    Expression System Strain: BL21 (DE3) RIL CODON PLUS
    Expression System Taxid: 469008
    Expression System Vector Type: PGEX-6P-1
    Fragment: UNP RESIDUES 333-420
    Gene: WT1
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: WT33
    Variant: -KTS
 
Molecule 2 - DNA (5'-D(*AP*GP*CP*GP*TP*GP*GP*GP*(5FC)P*GP*T)-3')
    Chains: B, E
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(*TP*AP*(5CM)P*GP*CP*CP*CP*AP*CP*GP*C)-3')
    Chains: C, F
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 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  (6, 15)

Asymmetric Unit (6, 15)
No.NameCountTypeFull Name
15CM2Mod. Nucleotide5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
25FC2Mod. Nucleotide5-FORMYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
3CA2Ligand/IonCALCIUM ION
4EDO2Ligand/Ion1,2-ETHANEDIOL
5NA1Ligand/IonSODIUM ION
6ZN6Ligand/IonZINC ION
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
15CM1Mod. Nucleotide5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
25FC1Mod. Nucleotide5-FORMYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
3CA-1Ligand/IonCALCIUM ION
4EDO1Ligand/Ion1,2-ETHANEDIOL
5NA-1Ligand/IonSODIUM ION
6ZN-1Ligand/IonZINC ION
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
15CM1Mod. Nucleotide5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
25FC1Mod. Nucleotide5-FORMYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
3CA-1Ligand/IonCALCIUM ION
4EDO1Ligand/Ion1,2-ETHANEDIOL
5NA-1Ligand/IonSODIUM ION
6ZN-1Ligand/IonZINC ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:355 , CYS A:360 , HIS A:373 , HIS A:377binding site for residue ZN A 501
02AC2SOFTWARECYS A:385 , CYS A:388 , HIS A:401 , HIS A:405binding site for residue ZN A 502
03AC3SOFTWARECYS A:413 , CYS A:418 , HIS A:431 , HIS A:435binding site for residue ZN A 503
04AC4SOFTWARECYS A:355 , CYS A:360 , HOH A:627 , HOH A:633binding site for residue CA A 504
05AC5SOFTWAREARG A:390 , HIS A:401 , DG B:4binding site for residue EDO A 505
06AC6SOFTWARECYS D:355 , CYS D:360 , HIS D:373 , HIS D:377binding site for residue ZN D 501
07AC7SOFTWARECYS D:385 , CYS D:388 , HIS D:401 , HIS D:405binding site for residue ZN D 502
08AC8SOFTWARECYS D:413 , CYS D:418 , HIS D:431 , HIS D:435binding site for residue ZN D 503
09AC9SOFTWAREHOH A:646 , CYS D:355 , CYS D:360 , HOH D:620 , HOH D:626binding site for residue CA D 504
10AD1SOFTWAREARG D:372 , SER D:393 , ARG D:394 , DG E:6 , HOH E:104binding site for residue EDO D 505
11AD2SOFTWAREDC F:6binding site for residue NA F 101
12AD3SOFTWARELYS D:351 , PHE D:364 , HIS D:369 , ARG D:372 , DG E:7 , DG E:10 , HOH E:112 , HOH E:116 , HOH E:121 , DG F:4 , DC F:5 , DC F:6binding site for Di-nucleotide DG E 8 and 5FC E 9
13AD4SOFTWARELYS D:351 , ARG D:366 , HIS D:369 , ARG D:372 , DG E:8 , DT E:11 , HOH E:111 , HOH E:112 , DA F:2 , 5CM F:3 , DG F:4binding site for Di-nucleotide 5FC E 9 and DG E 10
14AD5SOFTWAREARG D:366 , ASP D:368 , DA E:1 , DG E:10 , DT E:11 , DT F:1 , DG F:4 , HOH F:206 , HOH F:207 , HOH F:209binding site for Di-nucleotide DA F 2 and 5CM F 3
15AD6SOFTWAREASP D:368 , ARG D:372 , LYS D:399 , HOH D:616 , DG E:8 , 5FC E:9 , DG E:10 , DA F:2 , DC F:5binding site for Di-nucleotide 5CM F 3 and DG F 4

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5KL4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5KL4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5KL4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5KL4)

(-) Exons   (0, 0)

(no "Exon" information available for 5KL4)

(-) 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:90
                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....ee........ee.hhhhhhhhhhhhhh...ee......ee.hhhhhhhhhhhhhh...ee........ee.hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 5kl4 A 348 GSEKPYQCDFKDCERRFSRSDHLKRHQRRHTGVKPFQCKTCQRKFSRSDHLKTHTRTHTGEKPFSCRWPSCQKKFARSDELVRHHNMHQR 437
                                   357       367       377       387       397       407       417       427       437


Chain B from PDB  Type:DNA  Length:11
                                           
                 5kl4 B   1 AGCGTGGGxGT  11
                                    10 
                                    9-5FC


Chain C from PDB  Type:DNA  Length:11
                                           
                 5kl4 C   1 TAxGCCCACGC  11
                              |     10 
                              |        
                              3-5CM    


Chain D from PDB  Type:PROTEIN  Length:86
                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee........ee.hhhhhhhhhhhhhh...ee......ee.hhhhhhhhhhhhhh...ee........ee.hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                 5kl4 D 351 KPYQCDFKDCERRFSRSDHLKRHQRRHTGVKPFQCKTCQRKFSRSDHLKTHTRTHTGEKPFSCRWPSCQKKFARSDELVRHHNMHQ 436
                                   360       370       380       390       400       410       420       430      


Chain E from PDB  Type:DNA  Length:11
                                           
                 5kl4 E   1 AGCGTGGGxGT  11
                                    10 
                                    9-5FC


Chain F from PDB  Type:DNA  Length:11
                                           
                 5kl4 F   1 TAxGCCCACGC  11
                              |     10 
                              |        
                              3-5CM
   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 5KL4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5KL4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5KL4)

(-) Gene Ontology  (65, 65)

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
    5CM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    5FC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    AD1  [ RasMol ]  +environment [ RasMol ]
    AD2  [ RasMol ]  +environment [ RasMol ]
    AD3  [ RasMol ]  +environment [ RasMol ]
    AD4  [ RasMol ]  +environment [ RasMol ]
    AD5  [ RasMol ]  +environment [ RasMol ]
    AD6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5kl4)
 
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 | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites 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
  5kl4
    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
  WT1_HUMAN | P19544
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    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
  WT1_HUMAN | P19544
    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
        WT1_HUMAN | P19544: 1lu6 1xf7 2g7t 2g7v 2g7w 2g7x 2jp9 2jpa 2prt 3hpj 3myj 4r2e 4r2p 4r2q 4r2r 4r2s 4wuu 5kl2 5kl3 5kl5 5kl6 5kl7

(-) Related Entries Specified in the PDB File

5kl2 5kl3 5kl5 5kl6 5kl7