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 EPHRIN A2 (EPHA2) RECEPTOR PROTEIN KINASE WITH COMPOUND 2F
 
Authors :  D. Kudlinzki, V. L. Linhard, K. Witt, S. L. Gande, K. Saxena, S. Heinzlme G. Medard, B. Kuester, H. Schwalbe
Date :  31 Mar 17  (Deposition) - 07 Jun 17  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.76
Chains :  Asym./Biol. Unit :  A
Keywords :  Inhibitor, Complex, Protein Tyrosine Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Heinzlmeir, J. Lohse, T. Treiber, D. Kudlinzki, V. Linhard, S. L. Gande, S. Sreeramulu, K. Saxena, X. Liu, M. Wilhelm, H. Schwalbe, B. Kuster, G. Medard
Chemoproteomics-Aided Medicinal Chemistry For The Discovery Of Epha2 Inhibitors.
Chemmedchem V. 12 999 2017
PubMed-ID: 28544567  |  Reference-DOI: 10.1002/CMDC.201700217

(-) Compounds

Molecule 1 - EPHRIN TYPE-A RECEPTOR 2
    ChainsA
    EC Number2.7.10.1
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System CommonFALL ARMYWORM
    Expression System Taxid7108
    GeneEPHA2, ECK
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymEPITHELIAL CELL KINASE,TYROSINE-PROTEIN KINASE RECEPTOR ECK

 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
190Z1Ligand/Ion~{N}-(2-CHLORANYL-6-METHYL-PHENYL)-2-[[3-[(2,2,6,6-TETRAMETHYL-1-OXIDANYL-PIPERIDIN-4-YL)CARBAMOYL]PHENYL]AMINO]-1,3-THIAZOLE-5-CARBOXAMIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:619 , ALA A:644 , LYS A:646 , GLU A:663 , SER A:671 , ILE A:690 , THR A:692 , GLU A:693 , TYR A:694 , MET A:695 , GLU A:696 , ASN A:697 , GLY A:698 , GLU A:706 , LEU A:746 , SER A:756 , HOH A:1166 , HOH A:1227binding site for residue 90Z A 1001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5NK8)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Lys A:686 -Pro A:687

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5NK8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5NK8)

(-) Exons   (0, 0)

(no "Exon" information available for 5NK8)

(-) 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:266
                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhh.eeeeeeee..eeeeeeeehhhheeeeeeeeee....hhhhhhhhhhhhhhhh.........eeeee.....eeeeee.....hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5nk8 A 605 TTEIHPSCVTRQKVIGGEVYKGMLKTSSGKKEVPVAIKTLKAGYTEKQRVDFLGEAGIMGQFSHHNIIRLEGVISKYKPMMIITEYMENGALDKFLREKDGEFSVLQLVGMLRGIAAGMKYLANMNYVHRDLAARNILVNSNLVCKVSDFGPIRWTAPEAISYRKFTSASDVWSFGIVMWEVMTYGERPYWELSNHEVMKAINDGFRLPTPMDCPSAIYQLMMQCWQQERARRPKFADIVSILDKLIRAPDSLKTLADFDPRVSIR 894
                                   614     ||628       638       648       658       668       678       688       698       708       718       728       738       748       758||     788       798       808       818       828       838       848       858       868       878       888      
                                         620|                                                                                                                                   759|                                                                                                                  
                                          625                                                                                                                                    780                                                                                                                  

   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 5NK8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5NK8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5NK8)

(-) Gene Ontology  (62, 62)

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
    90Z  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Lys A:686 - Pro A:687   [ RasMol ]  
 

(-) 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
  5nk8
    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
  EPHA2_HUMAN | P29317
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.7.10.1
    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
  EPHA2_HUMAN | P29317
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        EPHA2_HUMAN | P293171mqb 2e8n 2k9y 2kso 2x10 2x11 3c8x 3czu 3fl7 3hei 3hpn 3kka 3mbw 3mx0 3skj 4p2k 4pdo 4trl 5ek7 5i9u 5i9v 5i9w 5i9x 5i9y 5i9z 5ia0 5ia1 5ia2 5ia3 5ia4 5ia5 5njz 5nk0 5nk1 5nk2 5nk3 5nk4 5nk5 5nk6 5nk7 5nk9 5nka 5nkb 5nkc 5nkd 5nke 5nkf 5nkg 5nkh 5nki

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5NK8)