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 :  HUMAN P38 MAP KINASE IN COMPLEX WITH DIBENZOSUBERONE COMPOUND 1
 
Authors :  S. C. Mayer-Wrangowski, D. Rauh
Date :  15 Sep 16  (Deposition) - 19 Apr 17  (Release) - 03 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Inhibitor, Dibenzosuberone, Human P38 Map Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. K. Wentsch, N. M. Walter, M. Buhrmann, S. Mayer-Wrangowski, D. Rauh G. J. R. Zaman, N. Willemsen-Seegers, R. C. Buijsman, M. Henning, D. Dauch, L. Zender, S. Laufer
Optimized Target Residence Time: Type I1/2 Inhibitors For P38 Alpha Map Kinase With Improved Binding Kinetics Through Direct Interaction With The R-Spine.
Angew. Chem. Int. Ed. Engl. V. 56 5363 2017
PubMed-ID: 28397331  |  Reference-DOI: 10.1002/ANIE.201701185

(-) Compounds

Molecule 1 - MITOGEN-ACTIVATED PROTEIN KINASE 14
    Chains: A
    EC Number: 2.7.11.24
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: MAPK14, CSBP, CSBP1, CSBP2, CSPB1, MXI2, SAPK2A
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: MAPK 14,CYTOKINE SUPPRESSIVE ANTI-INFLAMMATORY DRUG-BINDING PROTEIN,CSBP,MAP KINASE MXI2,MAX-INTERACTING PROTEIN 2,MITOGEN- ACTIVATED PROTEIN KINASE P38 ALPHA,MAP KINASE P38 ALPHA,STRESS- ACTIVATED PROTEIN KINASE 2A,SAPK2A

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
179Q1Ligand/Ion3-[(3-BENZAMIDO-4-FLUORANYL-PHENYL)AMINO]-~{N}-(2-MORPHOLIN-4-YLETHYL)-11-OXIDANYLIDENE-5,6-DIHYDRODIBENZO[1,2-~{D}:1',2'-~{F}][7]ANNULENE-9-CARBOXAMIDE
2BOG2Ligand/IonB-OCTYLGLUCOSIDE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:53 , GLU A:71 , LEU A:75 , ILE A:84 , THR A:106 , LEU A:108 , MET A:109 , GLY A:110 , LEU A:167 , ASP A:168 , PHE A:169 , LEU A:171 , HOH A:524 , HOH A:554binding site for residue 79Q A 401
2AC2SOFTWARETRP A:197 , HIS A:199 , LEU A:246 , LEU A:291 , ASP A:292 , SER A:293 , ASP A:294 , HOH A:532binding site for residue BOG A 402
3AC3SOFTWAREASN A:26 , TRP A:197 , LYS A:249 , ILE A:250 , SER A:251 , GLU A:336binding site for residue BOG A 403

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5TCO)

(-) 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:327
                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..eeeeee..eeeeeeee..eeeeee....eeeeeee......hhhhhhhhhhhhhhhhhh.......eeeee............eeeee....hhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee..........hhhhhh.......hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh..hhhhhh...hhhhhhhhhhh............hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhh...............hhhhhh..hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5tco A   6 PTFYRQELNKTIWEVPERYQNLSPVGSSVCAAFDTKTGLRVAVKKLSRPFQSIIHAKRTYRELRLLKHMKHENVIGLLDVFTPARSLEEFNDVYLVTHLMGADLNNIVKCQKLTDDHVQFLIYQILRGLKYIHSADIIHRDLKPSNLAVNEDCELKILDFGLTRWYRAPEIMLNWMHYNQTVDIWSVGCIMAELLTGRTLFPGTDHIDQLKLILRLVGTPGAELLKKISSESARNYIQSLTQMPKMNFANGANPLAVDLLEKMLVLDSDKRITAAQALAHAYFAQYHDPDDEPVADPYDQSFESRDLLIDEWKSLTYDEVISFVPPP 352
                                    15        25      ||39        49        59        69        79        89        99       109       119       129       139       149       159       169 ||    192       202       212       222       232       242       252       262       272|      285       295       305       315       325       335       345       
                                                     32|                                                                                                                                   171|                                                                                    272|                                                                            
                                                      37                                                                                                                                    185                                                                                     276
   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 5TCO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (84, 84)

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
    79Q  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    BOG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5tco)
 

(-) 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
  5tco
    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
  MK14_HUMAN | Q16539
    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)
  2.7.11.24
    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
  MK14_HUMAN | Q16539
    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
        MK14_HUMAN | Q16539: 1a9u 1bl6 1bl7 1bmk 1di9 1ian 1kv1 1kv2 1m7q 1ouk 1ouy 1ove 1oz1 1r39 1r3c 1w7h 1w82 1w83 1w84 1wbn 1wbo 1wbs 1wbt 1wbv 1wbw 1wfc 1yqj 1zyj 1zz2 1zzl 2baj 2bak 2bal 2baq 2fsl 2fsm 2fso 2fst 2gfs 2i0h 2lgc 2npq 2okr 2onl 2qd9 2rg5 2rg6 2y8o 2yis 2yiw 2yix 2zaz 2zb0 2zb1 3bv2 3bv3 3bx5 3c5u 3ctq 3d7z 3d83 3ds6 3dt1 3e92 3e93 3fc1 3fi4 3fkl 3fkn 3fko 3fl4 3fln 3flq 3fls 3flw 3fly 3flz 3fmh 3fmj 3fmk 3fml 3fmm 3fmn 3fsf 3fsk 3gc7 3gcp 3gcq 3gcs 3gcu 3gcv 3gfe 3gi3 3ha8 3hec 3heg 3hl7 3hll 3hp2 3hp5 3hrb 3hub 3huc 3hv3 3hv4 3hv5 3hv6 3hv7 3hvc 3iph 3itz 3iw5 3iw6 3iw7 3iw8 3k3i 3k3j 3kf7 3kq7 3l8s 3l8x 3lfa 3lfb 3lfc 3lfd 3lfe 3lff 3lhj 3mgy 3mh0 3mh1 3mh2 3mh3 3mpa 3mpt 3mvl 3mvm 3mw1 3new 3nnu 3nnv 3nnw 3nnx 3nww 3o8p 3o8t 3o8u 3obg 3obj 3oc1 3ocg 3od6 3ody 3odz 3oef 3pg3 3qud 3que 3rin 3roc 3s3i 3s4q 3u8w 3uvp 3uvq 3uvr 3zs5 3zsg 3zsh 3zsi 3zya 4a9y 4aa0 4aa4 4aa5 4aac 4dli 4dlj 4e5a 4e5b 4e6a 4e6c 4e8a 4eh2 4eh3 4eh4 4eh5 4eh6 4eh7 4eh8 4eh9 4ehv 4ewq 4f9w 4f9y 4fa2 4geo 4kin 4kip 4kiq 4l8m 4r3c 4zth 5eta 5etc 5etf 5eti 5ml5 5tbe

(-) Related Entries Specified in the PDB File

5tbe