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 PDK1 IN COMPLEX WITH ATP AND THE PIF-POCKET LIGAND RF4
 
Authors :  T. J. Rettenmaier, J. A. Wells
Date :  30 Jan 15  (Deposition) - 21 Oct 15  (Release) - 04 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Protein Kinase, Allostery, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. J. Rettenmaier, H. Fan, J. Karpiak, A. Doak, A. Sali, B. K. Shoichet, J. A. Wells
Small-Molecule Allosteric Modulators Of The Protein Kinase Pdk1 From Structure-Based Docking.
J. Med. Chem. V. 58 8285 2015
PubMed-ID: 26443011  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.5B01216

(-) Compounds

Molecule 1 - 3-PHOSPHOINOSITIDE-DEPENDENT PROTEIN KINASE 1
    Chains: A
    EC Number: 2.7.11.1
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Plasmid: PFASTBAC HTB
    Expression System Strain: SF9
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS PLASMID
    Fragment: UNP RESIDUES 50-359
    Gene: PDPK1, PDK1
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HPDK1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2GOL3Ligand/IonGLYCEROL
3RF42Ligand/Ion(2-{[2-(2,6-DIMETHYLPHENOXY)ETHYL]SULFANYL}-1H-BENZIMIDAZOL-1-YL)ACETIC ACID
4SEP1Mod. Amino AcidPHOSPHOSERINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:89 , GLY A:91 , SER A:92 , SER A:94 , VAL A:96 , ALA A:109 , LYS A:111 , SER A:160 , ALA A:162 , GLU A:166 , LEU A:212 , HOH A:662 , HOH A:677 , HOH A:680 , HOH A:720 , HOH A:724 , HOH A:730 , HOH A:734 , HOH A:760 , HOH A:761binding site for residue ATP A 401
2AC2SOFTWARELYS A:76 , LYS A:115 , ILE A:118 , VAL A:127 , ARG A:131 , THR A:148 , PHE A:149 , PHE A:157 , HOH A:665binding site for residue RF4 A 402
3AC3SOFTWAREARG A:172 , LEU A:254 , LYS A:257 , GLY A:278 , LEU A:279 , PHE A:291 , ILE A:295 , HOH A:526 , HOH A:660binding site for residue RF4 A 403
4AC4SOFTWAREALA A:103 , THR A:104 , SER A:105 , HIS A:139 , SER A:191 , TRP A:347 , GLU A:348 , ASN A:349 , LEU A:350 , HIS A:351 , HOH A:515binding site for residue GOL A 404
5AC5SOFTWAREPHE A:82 , LYS A:83 , PHE A:84 , GLU A:194 , GLY A:334 , LYS A:337 , HOH A:505 , HOH A:547 , HOH A:567binding site for residue GOL A 405
6AC6SOFTWAREPRO A:307 , LYS A:308binding site for residue GOL A 406

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4XX9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4XX9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4XX9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4XX9)

(-) Exons   (0, 0)

(no "Exon" information available for 4XX9)

(-) 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:289
                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhh.eeeeeeeee....eeeeeee.....eeeeeeeehhhhhhh.hhhhhhhhhhhhhh........eeeeee...eeeeee.....eehhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee...............hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh........hhhhhhhhhhhh..hhhhh..hhhhhhhhhhhhhhhhh.....hhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xx9 A  71 PPQPRKKRPEDFKFGKILGEGSFSTVVLARELATSREYAIKILEKRHIIKENKVPYVTRERDVMSRLDHPFFVKLYFTFQDDEKLYFGLSYAKNGELLKYIRKIGSFDETCTRFYTAEIVSALEYLHGKGIIHRDLKPENILLNEDMHIQITDFGTAKVLSPESKQARANsFVGTAQYVSPELLTEKSACKSSDLWALGCIIYQLVAGLPPFRAGNEGLIFAKIIKLEYDFPEKFFPKARDLVEKLLVLDATKRLGCEEMEGYGPLKAHPFFESVTWENLHQQTPPKLT 359
                                    80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240|      250       260       270       280       290       300       310       320       330       340       350         
                                                                                                                                                                                                    241-SEP
   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 4XX9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4XX9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4XX9)

(-) Gene Ontology  (56, 56)

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
    ATP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    RF4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SEP  [ 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 4xx9)
 

(-) 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
  4xx9
    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
  PDPK1_HUMAN | O15530
    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)
  2.7.11.1
    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
  PDPK1_HUMAN | O15530
    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
        PDPK1_HUMAN | O15530: 1h1w 1oky 1okz 1uu3 1uu7 1uu8 1uu9 1uvr 1w1d 1w1g 1w1h 1z5m 2biy 2pe0 2pe1 2pe2 2r7b 2vki 2xch 2xck 3h9o 3hrc 3hrf 3ion 3iop 3nax 3nay 3nun 3nus 3nuu 3nuy 3orx 3orz 3otu 3pwy 3qc4 3qcq 3qcs 3qcx 3qcy 3qd0 3qd3 3qd4 3rcj 3rwp 3rwq 3sc1 4a06 4a07 4aw0 4aw1 4ct1 4ct2 4rqk 4rqv 4rrv 5ack 5hkm 5hng 5ho7 5ho8 5lvl 5lvm 5lvn 5lvo 5lvp 5mrd

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4XX9)