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
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)

(-) Description

Title :  CRYSTAL STRUCTURE OF HYPER-PHOSPHORYLATED RET KINASE DOMAIN WITH (PROXIMAL) JUXTAMEMBRANE SEGMENT
 
Authors :  I. Plaza-Menacho, K. Barnouin, R. Barry, A. Borg, M. Orme, S. Mouillero R. J. Martinez-Torres, P. Meier, N. Q. Mcdonald
Date :  30 Oct 15  (Deposition) - 28 Dec 16  (Release) - 01 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.30
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Plaza-Menacho, K. Barnouin, R. Barry, A. Borg, M. Orme, R. Chauhan, S. Mouilleron, R. J. Martinez-Torres, P. Meier, N. Q. Mcdonald
Ret Functions As A Dual-Specificity Kinase That Requires Allosteric Inputs From Juxtamembrane Elements.
Cell Rep V. 17 3319 2016
PubMed-ID: 28009299  |  Reference-DOI: 10.1016/J.CELREP.2016.11.061

(-) Compounds

Molecule 1 - PROTO-ONCOGENE TYROSINE-PROTEIN KINASE RECEPTOR RET
    Chains: A
    EC Number: 2.7.10.1
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF21
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Fragment: UNP RESIDUES 659-1013
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CADHERIN FAMILY MEMBER 12, PROTO-ONCOGENE C-RET

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1PP11Ligand/Ion1-TER-BUTYL-3-P-TOLYL-1H-PYRAZOLO[3,4-D]PYRIMIDIN-4-YLAMINE
2PTR3Mod. Amino AcidO-PHOSPHOTYROSINE
3SEP1Mod. Amino AcidPHOSPHOSERINE
Biological Unit 1 (3, 10)
No.NameCountTypeFull Name
1PP12Ligand/Ion1-TER-BUTYL-3-P-TOLYL-1H-PYRAZOLO[3,4-D]PYRIMIDIN-4-YLAMINE
2PTR6Mod. Amino AcidO-PHOSPHOTYROSINE
3SEP2Mod. Amino AcidPHOSPHOSERINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:807 , LYS A:808 , GLY A:810 , VAL A:882 , ALA A:883 , GLU A:884 , GLY A:885BINDING SITE FOR RESIDUE PTR A 809
2AC2SOFTWAREARG A:873 , GLY A:894 , LEU A:895 , ARG A:897 , LYS A:907 , ARG A:908 , GLN A:910 , PTR A:928BINDING SITE FOR RESIDUE SEP A 909
3AC3SOFTWAREARG A:873 , ARG A:897 , SEP A:909 , GLY A:911 , MET A:918 , SER A:922 , HIS A:926 , ILE A:927 , THR A:929 , SER A:932BINDING SITE FOR RESIDUE PTR A 928
4AC4SOFTWARELEU A:730 , PHE A:735 , VAL A:738 , ALA A:756 , LYS A:758 , GLU A:775 , VAL A:804 , GLU A:805 , ALA A:807 , LEU A:881 , SER A:891BINDING SITE FOR RESIDUE PP1 A 2012
5AC5SOFTWAREPRO A:720 , ASN A:723 , HIS A:745 , ASP A:903 , SER A:904 , VAL A:906 , LYS A:907Binding site for Ligand PTR A 905 bound to SER A 904

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5FM2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5FM2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5FM2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5FM2)

(-) Exons   (0, 0)

(no "Exon" information available for 5FM2)

(-) 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:277
                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhh.eeeeeeeee....eeeeeeee.hhhh..eeeeeeee.....hhhhhhhhhhhhhhhhhh.......eeeee......eeee......hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee........eeee...eeee......ee...............hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5fm2 A  710 KILEDPKWEFPRKNLVLGKTLGEGEFGKVVKATAFHLKGRAGYTTVAVKMLKENASPSELRDLLSEFNVLKQVNHPHVIKLYGACSQDGPLLLIVEYAKyGSLRGFLRESALTMGDLISFAWQISQGMQYLAEMKLVHRDLAARNILVAEGRKMKISDFGLSRDVYEEDSyVKRsQGRIPVKWMAIESLFDHIyTTQSDVWSFGVLLWEIVTLGGNPYPGIPPERLFNLLKTGHRMERPDNCSEEMYRLMLQCWKQEPDKRPVFADISKDLEKMMVK 1011
                                   719       729       739       749       759       769       779       789       799       809       819|      854       864       874       884       894       904|   |  914       924   |   934       944       954       964       974       984       994      1004       
                                                                                                                             809-PTR   819|                                                         905-PTR                928-PTR                                                                               
                                                                                                                                        845                                                             909-SEP
   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 5FM2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5FM2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5FM2)

(-) Gene Ontology  (64, 64)

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
    PP1  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PTR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SEP  [ 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
(no "Cis Peptide Bonds" information available for 5fm2)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ 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 ](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
  5fm2
    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
  RET_HUMAN | P07949
    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)
  2.7.10.1
    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
  RET_HUMAN | P07949
    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
        RET_HUMAN | P07949: 1xpd 2ivs 2ivt 2ivu 2ivv 2x2k 2x2l 2x2m 2x2u 4cki 4ckj 4ux8 5amn 5fm3

(-) Related Entries Specified in the PDB File

5fm3 CRYSTAL STRUCTURE OF PHOSPHORYLATED RET TYROSINE KINASE JM-KD