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 MURINE NF-KAPPAB INDUCING KINASE (NIK) BOUND TO BENZOXEPIN COMPOUND 2
 
Authors :  M. A. Smith, P. A. Mcewan
Date :  08 Sep 16  (Deposition) - 11 Jan 17  (Release) - 08 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.32
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Protein Serine/Threonine Kinase, Nf-Kappab, Map3K14, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. M. Castanedo, N. Blaquiere, M. Beresini, B. Bravo, H. Brightbill, J. Chen, H. F. Cui, C. Eigenbrot, C. Everett, J. Feng, R. Godemann, E. Gogol, S. Hymowitz, A. Johnson, N. Kayagaki, P. B. Kohli, K. Knuppel J. Kraemer, S. Kruger, P. Loke, P. Mcewan, C. Montalbetti, D. A. Roberts, M. Smith, S. Steinbacher, S. Sujatha-Bhaskar, R. Takahashi, X. Wang, L. C. Wu, Y. Zhang, S. T. Staben
Structure-Based Design Of Tricyclic Nf-Kappa B Inducing Kinase (Nik) Inhibitors That Have High Selectivity Over Phosphoinositide-3-Kinase (Pi3K).
J. Med. Chem. V. 60 627 2017
PubMed-ID: 28005357  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.6B01363

(-) Compounds

Molecule 1 - MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 14
    Chains: A, B
    EC Number: 2.7.11.25
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF9
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Fragment: UNP RESIDUES 329-675
    Gene: MAP3K14, NIK
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090
    Synonym: NF-KAPPA-BETA-INDUCING KINASE,SERINE/THREONINE-PROTEIN KINASE NIK

 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  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
17742Ligand/Ion6,7-DIHYDROTHIENO[4,5]OXEPINO[1,2-~{C}]PYRIDINE-2-CARBOXAMIDE
2SO44Ligand/IonSULFATE ION
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
17741Ligand/Ion6,7-DIHYDROTHIENO[4,5]OXEPINO[1,2-~{C}]PYRIDINE-2-CARBOXAMIDE
2SO42Ligand/IonSULFATE ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
17741Ligand/Ion6,7-DIHYDROTHIENO[4,5]OXEPINO[1,2-~{C}]PYRIDINE-2-CARBOXAMIDE
2SO42Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:416 , ALA A:429 , MET A:471 , GLU A:472 , LEU A:473 , LEU A:474 , ASP A:521 , LEU A:524 , ASP A:536binding site for residue 774 A 701
2AC2SOFTWAREPRO A:406 , VAL A:408 , GLY A:409 , ARG A:410 , HIS A:417 , ARG A:418binding site for residue SO4 A 702
3AC3SOFTWAREARG A:637 , LYS A:638 , GLU A:639binding site for residue SO4 A 703
4AC4SOFTWAREARG B:637 , LYS B:638 , GLU B:639 , HIS B:642binding site for residue SO4 B 701
5AC5SOFTWAREHIS B:404 , PRO B:406 , VAL B:408 , GLY B:409 , VAL B:416 , HIS B:417 , ARG B:418 , HOH B:846binding site for residue SO4 B 702
6AC6SOFTWAREVAL B:416 , ALA B:429 , MET B:471 , GLU B:472 , LEU B:473 , LEU B:474 , ASP B:521 , LEU B:524 , ASP B:536binding site for residue 774 B 703

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5T8P)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5T8P)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5T8P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5T8P)

(-) Exons   (0, 0)

(no "Exon" information available for 5T8P)

(-) 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:327
                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh..eee.hhhhhhhhhhhhh.eeeee.................eee............eeeeee.....eeeeeeee.hhhhhhhhhh...........eeeeeee..eeeeee.....eehhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee......eee......ee................hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh..........hhhhhhhhh..hhhhh....hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5t8p A 333 VPVEEYLVHALQGSVSSGQAHSLASLAKTWSDNEGVLLTEKLKPVDYEYREEVHWMTHQPRVGRGSFGEVHRMKDKQTGFQCAVKKVRLEVFRVEELVACAGLSSPRIVPLYGAVREGPWVNIFMELLEGGSLGQLIKQMGCLPEDRALYYLGQALEGLEYLHTRRILHGDVKADNVLLSSDGSRAALCDFGHALCLQPDGLSLLTGDYIPGTETHMAPEVVMGKPCDAKVDIWSSCCMMLHMLNGCHPWTQYFRGPLCLKIASEPPPIREIPPSCAPLTAQAIQEGLRKEPVHRASAMELRRKVGKALQEVGGLKSPWKGEYKEPR 675
                                   342       352       362||     386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546 ||    558       568       578       588       598       608       618       628       638       648       658       668       
                                                        363|                                                                                                                                                                       548|                                                                                                                            
                                                         378                                                                                                                                                                        551                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:328
                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhh..eee.hhhhhhhhhhhhh.eeeee.................eee............eeeeee.....eeeeeeee.hhhhhhhhhh...........eeeeeee..eeeeee......hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee......eee......ee.......ee.........hhhhhhhhhhh..ee.hhhhhhhhhhhhhhhhhh..........hhhhhhhhh..hhhhh....hhhhhhhhhhhh........hhhhhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5t8p B 334 PVEEYLVHALQGSVSSGQAHSLASLAKTWSDNEGVLLTEKLKPVDYEYREEVHWMTHQPRVGRGSFGEVHRMKDKQTGFQCAVKKVRLEVFRVEELVACAGLSSPRIVPLYGAVREGPWVNIFMELLEGGSLGQLIKQMGCLPEDRALYYLGQALEGLEYLHTRRILHGDVKADNVLLSSDGSRAALCDFGHALCLQPDGLGKSLLTGDYIPGTETHMAPEVVMGKPCDAKVDIWSSCCMMLHMLNGCHPWTQYFRGPLCLKIASEPPPIREIPPSCAPLTAQAIQEGLRKEPVHRASAMELRRKVGKALQEVGGLKSPWKGEYKEPR 675
                                   343       353       363|      387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667        
                                                       363|                                                                                                                                                                                                                                                                                                         
                                                        378
   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 5T8P)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5T8P)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5T8P)

(-) Gene Ontology  (19, 19)

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
    774  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ 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 ]
    AC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5t8p)
 
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
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 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
  5t8p
    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
  M3K14_MOUSE | Q9WUL6
    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)
  2.7.11.25
    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
  M3K14_MOUSE | Q9WUL6
    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
        M3K14_MOUSE | Q9WUL6: 4g3c 4g3e 4g3f 4g3g 5t8o 5t8q

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5T8P)