Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit - manually
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit - manually
Asym./Biol. Unit - manually  (Jmol Viewer)
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 INHIBITOR OF KAPPAB KINASE BETA (I4122)
 
Authors :  G. Xu, Y. C. Lo, Q. Li, G. Napolitano, X. Wu, X. Jiang, M. Dreano, M. Karin,
Date :  11 May 11  (Deposition) - 25 May 11  (Release) - 25 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  4.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Kinase Uld, Kinase Ubiquitin-Like Domain Scaffold Helix, Kinase, I Kappa B Alpha, Phosphorylation, Immune System, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  G. Xu, Y. C. Lo, Q. Li, G. Napolitano, X. Wu, X. Jiang, M. Dreano, M. Karin H. Wu
Crystal Structure Of Inhibitor Of Kappab Kinase Beta.
Nature V. 472 325 2011
PubMed-ID: 21423167  |  Reference-DOI: 10.1038/NATURE09853

(-) Compounds

Molecule 1 - MGC80376 PROTEIN
    ChainsA
    MutationYES
    Organism CommonCLAWED FROG,COMMON PLATANNA,PLATANNA
    Organism ScientificXENOPUS LAEVIS
    Organism Taxid8355

 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
1XNM1Ligand/Ion(4-{[4-(4-CHLOROPHENYL)PYRIMIDIN-2-YL]AMINO}PHENYL)[4-(2-HYDROXYETHYL)PIPERAZIN-1-YL]METHANONE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:21 , VAL A:29 , ALA A:42 , MET A:96 , GLU A:97 , TYR A:98 , CYS A:99 , GLY A:102 , ASP A:103 , LYS A:106 , VAL A:152BINDING SITE FOR RESIDUE XNM A 676

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3RZF)

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Ser A:51 -Pro A:52
2Pro A:221 -Phe A:222
3Pro A:228 -Val A:229
4Thr A:344 -Gly A:345
5Asn A:362 -Ser A:363

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3RZF)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3RZF)

(-) Exons   (0, 0)

(no "Exon" information available for 3RZF)

(-) 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:541
 aligned with Q6INT1_XENLA | Q6INT1 from UniProtKB/TrEMBL  Length:742

    Alignment length:622
                             1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619  
         Q6INT1_XENLA     - -MKERLGTGGFGYVLRWIHQDTGEQVAIKQCRQELSPKNRERWCLEIQIMKKLNHPNVVSAREVPDGLQKLAPNDLPLLAMEYCEGGDLRKYLNQFENCCGLKEGPIRTLLSDISSALRYLHENRIIHRDLKPENIVLQPGPQRLIHKIIDLGYAKELDQGSLCTSFVGTLQYLAPELLEQKKYTVTVDYWSFGTLAFECITGFRPFLPNWQPVQWHGKVREKSNEHIVVYDDLTGAVKFSSVLPTPNHLSGILAGKLERWLQCMLMWHQRQRGTDPQNPNVGCFQALDSILSLKLLSVMNMVSGRVHTYPVTENENLQNLKSWLQQDTGIPEEEQELLQASGLALNSAQPLTQYVIDCTVIDGRQGEGDLIFLFDNRKTVYEPQISLPAHPESVSIVLQDPKRPLTYTHLRRVWGQIWQTIRALKEDCARLLQGQRTSMVNLLRYNTELSKKKNSMTSECEQLKAKLDFFRSSIQIDLEKYSEQMEFGITSEKLLSAWREMEQAVELCGREREVQALVDKMMALQTDSVDLQRNPLGRKHRGTLDDLEEQARDLYRRLRERPRDQRTPGDSNDMVRLLILAIQSFEKRVILIYDQLSKTVVCKRKALELSPKVKEVMNLMR 621
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -Pkinase-3rzfA01 A:17-295                                                                                                                                                                                                                                                               ---------------------------------------------------------------------------------       -----------      ---------------------------------------------------------------------------                                                    ------------------------       ------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee..eeeeeee......eeeeeee.....hhhhhhhhhhhhhhhhh.........................eeee.....hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh...........eeee......eeee.........................hhhhhh.....hhhhhhhhhhhhhhhhhh..................------.........................hhhhhhhhhhhhh......---..........hhhhhhhhhh.ee.eee....ee..ee.....hhhhhhhhhhh....hhhhheeee..........hhhhh......-------..eeee.....------........hhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.....----------------------------------------------------.............hhhhhh.....-------.hhhhhhhhhhhh.................hhhhhhhhhhh.....hhhhhhhhhhhh.........hhhhhh...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rzf A  16 EMKERLGTGGFGYVLRWIHQDTGEQVAIKQCRQELSPKNRERWCLEIQIMKKLNHPNVVSAREVPDGLQKLAPNDLPLLAMEYCEGGDLRKYLNQFENCCGLKEGPIRTLLSDISSALRYLHENRIIHRDLKPENIVLQPGPQRLIHKIIDLGYAKELDQGELCTEFVGTLQYLAPELLEQKKYTVTVDYWSFGTLAFECITGFRPFLPNWQPVQWHGKVR------IVVYDDLTGAVKFSSVLPTPNHLSGILAGKLERWLQCMLMWHQR---TDPQNPNVGCFQALDSILSLKLLSVMNMVSGRVHTYPVTENENLQNLKSWLQQDTGIPEEEQELLQASGLALNSAQPLTQYVIDCTV-------GDLIFLFDNRK------ISLPAHPESVSIVLQDPKRPLTYTHLRRVWGQIWQTIRALKEDCARLLQGQRTSMVNLLRYNTELSKKKNSMTSE----------------------------------------------------REVQALVDKMMALQTDSVDLQRNP-------TLDDLEEQARDLYRRLRERPRDQRTPGDSNDMVRLLILAIQSFEKRVILIYDQLSKTVVCKRKALELSPKVKEVMNLMR 637
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235|      245       255       265       275       285|   |  295       305       315       325       335       345       355       365       375|      385        |-     | 405       415       425       435       445       455       465       475         -         -         -         -         -  |    535       545     |   -   |   565       575       585       595       605       615       625       635  
                                                                                                                                                                                                                                                      236    243                                        286 290                                                                                   376     384       394    401                                                                       475                                                  528                    551     559                                                                              

   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 3RZF)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3RZF)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: PKinase (934)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q6INT1_XENLA | Q6INT1)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0008384    IkappaB kinase activity    Catalysis of the reaction: ATP + IkappaB protein = ADP + IkappaB phosphoprotein.
    GO:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
biological process
    GO:0007252    I-kappaB phosphorylation    The process of introducing a phosphate group into an inhibitor of kappa B (I-kappaB) protein. Phosphorylation of I-kappaB targets I-kappaB for ubiquitination and proteasomal degradation, thus releasing bound NF-kappaB dimers, which can translocate to the nucleus to bind DNA and regulate transcription.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
cellular component
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

 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
    XNM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Asn A:362 - Ser A:363   [ RasMol ]  
    Pro A:221 - Phe A:222   [ RasMol ]  
    Pro A:228 - Val A:229   [ RasMol ]  
    Ser A:51 - Pro A:52   [ RasMol ]  
    Thr A:344 - Gly A:345   [ 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
  3rzf
    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
  Q6INT1_XENLA | Q6INT1
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/TrEMBL
 
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
  Q6INT1_XENLA | Q6INT1
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q6INT1_XENLA | Q6INT13qa8

(-) Related Entries Specified in the PDB File

3qa8