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

(-) Description

Title :  CRYSTAL STRUCTURE OF PEPTIDE INHIBITOR-FREE GSK-3/AXIN COMPLEX
 
Authors :  M. L. -H. Chu, J. L. Stamos, M. D. Enos, N. Shah, W. I. Weis
Date :  14 Nov 13  (Deposition) - 26 Mar 14  (Release) - 23 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Wnt, Lrp6, Auto-Inhibited, Gsk-3, Axin, Kinase, Primed Substrate, Transferase-Peptide Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. L. Stamos, M. L. Chu, M. D. Enos, N. Shah, W. I. Weis
Structural Basis Of Gsk-3 Inhibition By N-Terminal Phosphorylation And By The Wnt Receptor Lrp6.
Elife V. 3 01998 2014
PubMed-ID: 24642411

(-) Compounds

Molecule 1 - GLYCOGEN SYNTHASE KINASE-3 BETA
    Chains: A
    EC Number: 2.7.11.26, 2.7.11.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET29B(+)
    Expression System Strain: BL21(DE3) CODON-PLUS RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 1-383
    Gene: GSK3B
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: GSK-3 BETA, SERINE/THREONINE-PROTEIN KINASE GSK3B
 
Molecule 2 - AXIN-1
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: MODIFIED PGEX-KG
    Expression System Strain: BL21(DE3) CODON-PLUS RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 383-402
    Gene: AXIN, AXIN1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: AXIS INHIBITION PROTEIN 1, HAXIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 10)

Asymmetric/Biological Unit (5, 10)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2CL1Ligand/IonCHLORIDE ION
3DTT1Ligand/Ion2,3-DIHYDROXY-1,4-DITHIOBUTANE
4GOL5Ligand/IonGLYCEROL
5MG2Ligand/IonMAGNESIUM ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:56 , LYS A:86 , SER A:118 , ASN A:129BINDING SITE FOR RESIDUE GOL A 401
02AC2SOFTWAREASP A:49 , ARG A:50 , TYR A:146 , TYR A:157 , TYR A:161 , PRO A:191BINDING SITE FOR RESIDUE GOL A 402
03AC3SOFTWAREARG A:144 , SER A:147 , ARG A:148 , LEU A:252 , GLN A:254 , PRO A:255 , VAL A:304 , HOH A:621BINDING SITE FOR RESIDUE GOL A 403
04AC4SOFTWAREARG A:96 , ARG A:180 , LYS A:205 , ASN A:213 , VAL A:214BINDING SITE FOR RESIDUE GOL A 404
05AC5SOFTWARELYS A:292 , PRO A:294 , HOH A:535 , GLU B:397BINDING SITE FOR RESIDUE GOL A 405
06AC6SOFTWAREASP A:200 , ADP A:408BINDING SITE FOR RESIDUE MG A 406
07AC7SOFTWARELYS A:183 , ASN A:186 , ASP A:200 , ADP A:408BINDING SITE FOR RESIDUE MG A 407
08AC8SOFTWAREPHE A:67 , ALA A:83 , LYS A:85 , LEU A:132 , ASP A:133 , TYR A:134 , VAL A:135 , THR A:138 , ARG A:141 , GLN A:185 , ASN A:186 , ASP A:200 , MG A:406 , MG A:407 , HOH A:549 , HOH A:622BINDING SITE FOR RESIDUE ADP A 408
09AC9SOFTWAREARG A:319 , THR A:326 , ALA A:327 , ARG A:328 , GLU A:333BINDING SITE FOR RESIDUE DTT A 409
10BC1SOFTWARELYS A:297BINDING SITE FOR RESIDUE CL A 410

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4NM0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4NM0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4NM0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4NM0)

(-) Exons   (0, 0)

(no "Exon" information available for 4NM0)

(-) 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:356
                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains d4nm0a_ A: Glycogen synthase kinase-3 beta (Gsk3b)                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee....eeeeeeee.......eeeeeeeeeeeee...eeeeeeee.....eeeeeeeee.....hhhhhhhh.........eeeeeeee......eeeeeeee...eehhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee......eee......ee.................hhhhhh......hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh..hhhhhhhhhhhhh..........hhhhhh....hhhhhhhhhh....hhhhh.hhhhhhhhhhhhhhhh........................hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nm0 A  26 MKVSRDSKVTTVVATPGQGPDRPQEVSYTDTKVIGNGSFGVVYQAKLCDSGELVAIKKVLQDKRFKNRELQIMRKLDHCNIVRLRYFFYSSGEKKDEVYLNLVLDYVPETVYRVARHYSRAKQTLPVIYVKLYMYQLFRSLAYIHSFGICHRDIKPQNLLLDPDTAVLKLCDFGSAKQLVRGEPNVSYICSRYYRAPELIFGATDYTSSIDVWSAGCVLAELLLGQPIFPGDSGVDQLVEIIKVLGTPTREQIREMNPNYTEFKFPQIKAHPWTKVFRPRTPPEAIALCSRLLEYTPTARLTPLEACAHSFFDELRDPNVKLPNGRDTPALFNFTTQELSSNPPLATILIPPHARH 384
                                 || 38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378      
                                31|                                                                                                                                                                                                                                                                                                                                                             
                                 35                                                                                                                                                                                                                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:21
                                                     
               SCOP domains --------------------- SCOP domains
               CATH domains --------------------- CATH domains
               Pfam domains --------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------- SAPs(SNPs)
                    PROSITE --------------------- PROSITE
                 Transcript --------------------- Transcript
                 4nm0 B 381 ILVEPQKFAEELIHRLEAVQR 401
                                   390       400
   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  (1, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4NM0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4NM0)

(-) Gene Ontology  (193, 215)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    ADP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    DTT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ 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 ]
    BC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4nm0)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites 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
  4nm0
    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
  AXIN1_HUMAN | O15169
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  GSK3B_HUMAN | P49841
    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)
  2.7.11.1
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
  2.7.11.26
    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
  AXIN1_HUMAN | O15169
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  GSK3B_HUMAN | P49841
    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
        AXIN1_HUMAN | O15169: 1dk8 1emu 1o9u 3zdi 4b7t 4nm3 4nm5 4nm7 4nu1
        GSK3B_HUMAN | P49841: 1gng 1h8f 1i09 1j1b 1j1c 1o6k 1o6l 1o9u 1pyx 1q3d 1q3w 1q41 1q4l 1q5k 1r0e 1uv5 2jdo 2jdr 2jld 2o5k 2ow3 2uw9 2x39 2xh5 3cqu 3cqw 3du8 3e87 3e88 3e8d 3f7z 3f88 3gb2 3i4b 3l1s 3m1s 3mv5 3ow4 3pup 3q3b 3qkk 3say 3sd0 3zdi 3zrk 3zrl 3zrm 4acc 4acd 4acg 4ach 4afj 4b7t 4dit 4ekk 4iq6 4j1r 4j71 4nm3 4nm5 4nm7 4ptc 4pte 4ptg 5f94 5f95 5hln 5hlp 5k5n

(-) Related Entries Specified in the PDB File

4nm3 THE SAME PROTEIN COMPLEXED WITH ITS OWN PHOSPHORYLATED N- TERMINAL AUTO-INHIBITORY PS9 PEPTIDE BUT WITHOUT ALF3
4nm5 THE SAME PROTEIN COMPLEXED WITH PHOSPHORYLATED WNT RECEPTOR LRP6 C-MOTIF
4nm7 THE SAME PROTEIN COMPLEXED WITH PHOSPHORYLATED WNT RECEPTOR LRP6 E-MOTIF
4nu1 THE SAME PROTEIN COMPLEXED WITH ITS OWN PHOSPHORYLATED N- TERMINAL AUTO-INHIBITORY PS9 PEPTIDE AND ALF3 IS A TRANSITION STATE MIMICRY