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 MST2 IN COMPLEX WITH XMU-MP-1
 
Authors :  L. L. Kong, C. H. Yun
Date :  29 Aug 15  (Deposition) - 31 Aug 16  (Release) - 31 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.47
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Mst2, Mst1, Hippo Pathway, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  F. Fan, Z. He, L. L. Kong, Q. Chen, Q. Yuan, S. Zhang, J. Ye, H. Liu, X. Sun, J. Geng, L. Yuan, L. Hong, C. Xiao, W. Zhang, X. Sun, Y. Li, P. Wang, L. Huang, X. Wu, Z. Ji, Q. Wu, N. S. Xia, N. S. Gray, L. Chen, C. H. Yun, X. Deng, D. Zhou
Pharmacological Targeting Of Kinases Mst1 And Mst2 Augments Tissue Repair And Regeneration
Sci Transl Med V. 8 Ra108 2016
PubMed-ID: 27535619  |  Reference-DOI: 10.1126/SCITRANSLMED.AAF2304

(-) Compounds

Molecule 1 - SERINE/THREONINE-PROTEIN KINASE 3
    ChainsA, B
    EC Number2.7.11.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET-28A
    Expression System StrainBL21 (DE3)
    Expression System Taxid469008
    GeneSTK3, KRS1, MST2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMAMMALIAN STE20-LIKE PROTEIN KINASE 2,MST-2,STE20-LIKE KINASE MST2,SERINE/THREONINE-PROTEIN KINASE KRS-1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
15BS2Ligand/Ion4-[(5,10-DIMETHYL-6-OXO-6,10-DIHYDRO-5H-PYRIMIDO[5,4-B]THIENO[3,2-E][1,4]DIAZEPIN-2-YL)AMINO]BENZENESULFONAMIDE
2CL1Ligand/IonCHLORIDE ION
3SO41Ligand/IonSULFATE ION
4TPO4Mod. Amino AcidPHOSPHOTHREONINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:33 , GLU A:100 , TYR A:101 , CYS A:102 , GLY A:103 , GLY A:105 , ASP A:109 , LEU A:153 , ASP A:164binding site for residue 5BS A 401
2AC2SOFTWARELYS A:132binding site for residue CL A 402
3AC3SOFTWARELEU B:33 , VAL B:41 , ALA B:54 , GLU B:100 , TYR B:101 , CYS B:102 , ASP B:109 , LEU B:153 , ALA B:163 , LYS B:298 , HOH B:525binding site for residue 5BS B 401
4AC4SOFTWARECYS B:102 , GLY B:103 , ASN B:155 , THR B:156binding site for residue SO4 B 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5DH3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5DH3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5DH3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5DH3)

(-) Exons   (0, 0)

(no "Exon" information available for 5DH3)

(-) 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:289
                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhheeeeeeeee....eeeeeee....eeeeeeeee...hhhhhhhhhhhhhhh.......eeeeeee..eeeeeee....eehhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee.............hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh...........hhhhhhhhhhhh........hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dh3 A  19 LTKQPEEVFDVLEKLGEGSYGSVFKAIHKESGQVVAIKQVPVESDLQEIIKEISIMQQCDSPYVVKYYGSYFKNTDLWIVMEYCGAGSVSDIIRLRNKTLIEDEIATILKSTLKGLEYLHFMRKIHRDIKAGNILLNTEGHAKLADFGVAGQLTDtMAKRNtVIGTPFWMAPEVIQEIGYNCVADIWSLGITSIEMAEGKPPYADIHPMRAIFMIPTNPPPTFRKPELWSDDFTDFVKKCLVKNPEQRATATQLLQHPFIKNAKPVSILRDLITEAMEIKAKRHEEQQR 307
                                    28        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         
                                                                                                                                                                                     174-TPO |                                                                                                                               
                                                                                                                                                                                           180-TPO                                                                                                                           

Chain B from PDB  Type:PROTEIN  Length:285
                                                                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhheeeeeeeeee..eeeeeeee.....eeeeeee....hhhhhhhhhhhhhhh.......eeeeeee..eeeeeee....eehhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee.............hhhhhhhhhhh......hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh...........hhhhhhhhhhhh........hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dh3 B  18 SLTKQPEEVFDVLEKLGEGSYGSVFKAIHKESGQVVAIKQVPVESDLQEIIKEISIMQQCDSPYVVKYYGSYFKNTDLWIVMEYCGAGSVSDIIRLRNKTLIEDEIATILKSTLKGLEYLHFMRKIHRDIKAGNILLNTEGHAKLADFGVAGQLTDtMAKRNtVIGTPFWMAPEVIQEIGYNCVADIWSLGITSIEMAEGKPPYADIHPMRAIFMIPTNPPPTFRKPELWSDDFTDFVKKCLVKNPEQRATATQLLQHPFIKNAKPVSILRDLITEAMEIKAKRH 302
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167      |177  |    187       197       207       217       227       237       247       257       267       277       287       297     
                                                                                                                                                                                      174-TPO |                                                                                                                          
                                                                                                                                                                                            180-TPO                                                                                                                      

   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 5DH3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5DH3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5DH3)

(-) Gene Ontology  (42, 42)

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
    5BS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    TPO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5dh3)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5dh3
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  STK3_HUMAN | Q13188
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.7.11.1
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  STK3_HUMAN | Q13188
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        STK3_HUMAN | Q131883wws 4hkd 4l0n 4lg4 4lgd 4oh9 5brm

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5DH3)