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 :  CRYSTAL STRUCTURE OF SPINDLIN1 BOUND TO COMPOUND EML631
 
Authors :  X. Su, H. Li
Date :  08 May 16  (Deposition) - 24 May 17  (Release) - 24 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Tudor Domain, Cell Cycle (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Bae, M. Viviano, X. Su, J. Lu, D. Cheng, C. Sagum, S. Castellano, X. Bai, C. Johnson, M. I. Khalil, J. Shen, K. Chen, H. Li, G. Sbardella, M. T. Bedford
Envolving Spindlin1 Small Molecular Inhibitors Using Protei Microarrays
Nat. Chem. Biol. 2017
PubMed: search  |  Reference-DOI: 10.1038/NCHEMBIO.2377

(-) Compounds

Molecule 1 - SPINDLIN-1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidRSFDUET
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentSPIN/SSTY REPEATS, UNP RESIDUES 50-262
    GeneSPIN1, OCR, SPIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymOVARIAN CANCER-RELATED PROTEIN,SPINDLIN1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
16PD2Ligand/Ion[4-(2-PYRROLIDIN-1-YLETHYL)PIPERIDIN-1-YL]-[4-[4-(2-PYRROLIDIN-1-YLETHYL)PIPERIDIN-1-YL]CARBONYL-3-[[4-(PYRROLIDIN-1-YLMETHOXY)PHENYL]AMINO]PHENYL]METHANONE
2CL2Ligand/IonCHLORIDE ION
3MG1Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
16PD1Ligand/Ion[4-(2-PYRROLIDIN-1-YLETHYL)PIPERIDIN-1-YL]-[4-[4-(2-PYRROLIDIN-1-YLETHYL)PIPERIDIN-1-YL]CARBONYL-3-[[4-(PYRROLIDIN-1-YLMETHOXY)PHENYL]AMINO]PHENYL]METHANONE
2CL-1Ligand/IonCHLORIDE ION
3MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
16PD1Ligand/Ion[4-(2-PYRROLIDIN-1-YLETHYL)PIPERIDIN-1-YL]-[4-[4-(2-PYRROLIDIN-1-YLETHYL)PIPERIDIN-1-YL]CARBONYL-3-[[4-(PYRROLIDIN-1-YLMETHOXY)PHENYL]AMINO]PHENYL]METHANONE
2CL-1Ligand/IonCHLORIDE ION
3MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:60 , TRP A:62 , TRP A:72 , TYR A:91 , PHE A:94 , CYS A:96 , TYR A:98 , LEU A:100 , PHE A:141 , TRP A:151 , ASP A:173 , TYR A:177 , TYR A:179 , HIS A:252 , HOH A:417 , HOH A:419 , HOH A:431binding site for residue 6PD A 301
2AC2SOFTWAREHOH A:405 , HOH A:407 , HOH A:423 , HOH B:420 , HOH B:423 , HOH B:429binding site for residue MG A 302
3AC3SOFTWAREARG A:152 , LYS A:172binding site for residue CL A 303
4AC4SOFTWARETRP B:62 , TRP B:72 , TYR B:91 , PHE B:94 , CYS B:96 , TYR B:98 , LEU B:100 , PHE B:141 , TRP B:151 , TYR B:170 , ASP B:173 , TYR B:177 , TYR B:179 , HIS B:252 , HOH B:416 , HOH B:434binding site for residue 6PD B 301
5AC5SOFTWAREHOH A:405 , ARG B:152 , LYS B:172binding site for residue CL B 302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Glu A:223 -Asp A:224

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5JSJ)

(-) 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:195
                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeee.....eeeeeeeeeee......eeeeee......eeee......eeeeee...........hhhhhhhhh..eeeeeee.....eeeeeeeeeee.......eeeee......eeehhhhhhhh..eee........eeeee.....eeeeeeeee......eeeeee......eeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jsj A  49 SRRNIVGCRIQHGWKEGNGPVTQWKGTVLDQVPVNPSLYLIKYDGFDCVYGLELNKDERVSALEVLPDRVATSRISDAHLADTMIGKAVEHMFETEDGSKDEWRGMVLARAPVMNTWFYITYEKDPVLYMYQLLDDYKEGDLRIMPDSLVGKQVEYAKEDGSKRTGMVIHQVEAKPSVYFIKFDDDFHIYVYDLV 259
                                    58        68        78        88        98       108       118       128       138       148       158       168       178       188      |214       224       234       244       254     
                                                                                                                                                                            195|                                               
                                                                                                                                                                             212                                               

Chain B from PDB  Type:PROTEIN  Length:196
                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeee.......eeeeeeeeee.......eeeee......eee.......eeeeee...........hhhhhhhhh..eeeeeee.....eeeeeeeeeee.......eeeee..eeeeeeehhhhhhhh..eee........eeeeee...eeeeeeeeee......eeeeee.....eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jsj B  48 GSRRNIVGCRIQHGWKEGNGPVTQWKGTVLDQVPVNPSLYLIKYDGFDCVYGLELNKDERVSALEVLPDRVATSRISDAHLADTMIGKAVEHMFETEDGSKDEWRGMVLARAPVMNTWFYITYEKDPVLYMYQLLDDYKEGDLRIMPDSLVGKQVEYAKEDGSKRTGMVIHQVEAKPSVYFIKFDDDFHIYVYDLV 259
                                    57        67        77        87        97       107       117       127       137       147       157       167       177       187      |213       223       233       243       253      
                                                                                                                                                                            194|                                                
                                                                                                                                                                             211                                                

   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 5JSJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

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
    6PD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ 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 ]
 
  Cis Peptide Bonds
    Glu A:223 - Asp A:224   [ RasMol ]  
 
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
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5jsj
    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
  SPIN1_HUMAN | Q9Y657
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    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
  SPIN1_HUMAN | Q9Y657
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        SPIN1_HUMAN | Q9Y6572ns2 4h75 4mzf 4mzg 4mzh 5jsg

(-) Related Entries Specified in the PDB File

5jsg THE SAME PROTEIN BOUND TO A DIFFERENT COMPOUND