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 AN INHIBITOR-BOUND SYK
 
Authors :  S. J. Lee, J. Choi, B. G. Han, H. Song, J. S. Koh, B. I. Lee
Date :  30 Dec 14  (Deposition) - 30 Dec 15  (Release) - 19 Oct 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Syk Kinase, Inhibitor, Spleen Tyrosine Kinase, Transferase- Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. J. Lee, J. S. Choi, B. G. Han, H. S. Kim, H. J. Song, J. Lee, S. Nam, S. H. Goh, J. H. Kim, J. S. Koh, B. I. Lee
Crystal Structures Of Spleen Tyrosine Kinase In Complex Wit Novel Inhibitors: Structural Insights For Design Of Anticancer Drugs
Febs J. V. 283 3613 2016
PubMed-ID: 27504936  |  Reference-DOI: 10.1111/FEBS.13831

(-) Compounds

Molecule 1 - TYROSINE-PROTEIN KINASE SYK
    Chains: A
    EC Number: 2.7.10.2
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Plasmid: PVL1393
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Fragment: PROTEIN KINASE DOMAIN, RESIDUES 356-635
    Gene: SYK
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SPLEEN TYROSINE KINASE,P72-SYK

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1X4G1Ligand/Ion(3R)-1-{[1-(5-FLUORO-2-{[4-(2-HYDROXYETHOXY)-3,5-DIMETHYLPHENYL]AMINO}PYRIMIDIN-4-YL)-4-METHYL-1H-PYRROL-3-YL]METHYL}PYRROLIDIN-3-OL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:377 , ALA A:400 , VAL A:433 , MET A:448 , GLU A:449 , MET A:450 , ALA A:451 , GLU A:452 , GLY A:454 , PRO A:455 , ARG A:498 , ASN A:499 , LEU A:501 , ASP A:512 , HOH A:848binding site for residue X4G A 701

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4XG4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4XG4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4XG4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4XG4)

(-) Exons   (0, 0)

(no "Exon" information available for 4XG4)

(-) 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:264
                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhh.eeeeeeeeeee..eeeeeeeee....eeeeeeeee...hhhhhhhhhhhhhh........eeeeee...eeeeee....eehhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eeeee..eeee......ee.......ee...hhhhhhhhhhhhheehhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4xg4 A 363 VYLDRKLLTLEDKELGSGNFGTVKKGYYQMKKVVKTVAVKILKPALKDELLAEANVMQQLDNPYIVRMIGICEAESWMLVMEMAELGPLNKYLQQNRHVKDKNIIELVHQVSMGMKYLEESNFVHRDLAARNVLLVTQHYAKISDFGLSKALRADENYYKAKWPVKWYAPECINYYKFSSKSDVWSFGVLMWEAFSYGQKPYRGMKGSEVTAMLEKGERMGCPAGCPREMYDLMNLCWTYDVENRPGFAAVELRLRNYYYDVVN 635
                                   372       382       392       402  ||   417       427       437       447       457       467       477       487       497       507       517       527||     541       551       561       571       581       591       601       611       621       631    
                                                                    405|                                                                                                                  528|                                                                                                      
                                                                     411                                                                                                                   533
   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 4XG4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4XG4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4XG4)

(-) Gene Ontology  (87, 87)

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
    X4G  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4xg4)
 

(-) 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
  4xg4
    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
  KSYK_HUMAN | P43405
    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)
  2.7.10.2
    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
  KSYK_HUMAN | P43405
    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
        KSYK_HUMAN | P43405: 1a81 1csy 1csz 1xba 1xbb 1xbc 3buw 3emg 3fqe 3fqh 3fqs 3srv 3tub 3tuc 3tud 3vf8 3vf9 4dfl 4dfn 4f4p 4fl1 4fl2 4fl3 4fyn 4fyo 4fz6 4fz7 4gfg 4i0r 4i0s 4i0t 4puz 4pv0 4px6 4rss 4rx7 4rx8 4rx9 4wnm 4xg2 4xg3 4xg6 4xg7 4xg8 4xg9 4yjo 4yjp 4yjq 4yjr 4yjs 4yjt 4yju 4yjv 5c26 5c27 5cxh 5cxz 5cy3 5ghv 5lma 5lmb 5t68 5tiu 5tr6 5tt7

(-) Related Entries Specified in the PDB File

4xg2 4xg3 4xg5 4xg6 4xg7 4xg8 4xg9