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(-) Description

Title :  CRYSTAL STRUCTURE OF PDK1 IN COMPLEX WITH ATP AND PIFTIDE
 
Authors :  T. J. Rettenmaier, J. A. Wells
Date :  06 Nov 14  (Deposition) - 17 Dec 14  (Release) - 14 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.41
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein Kinase, Piftide, Phosphorylation, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. J. Rettenmaier, J. D. Sadowsky, N. D. Thomsen, S. C. Chen, A. K. Doak, M. R. Arkin, J. A. Wells
A Small-Molecule Mimic Of A Peptide Docking Motif Inhibits The Protein Kinase Pdk1.
Proc. Natl. Acad. Sci. Usa V. 111 18590 2014
PubMed-ID: 25518860  |  Reference-DOI: 10.1073/PNAS.1415365112

(-) 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 Common: FALL ARMYWORM
    Expression System Plasmid: PFASTBAC HTB
    Expression System Strain: SF9
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Fragment: CATALYTIC DOMAIN (UNP RESIDUES 50-359)
    Gene: PDK1, PDPK1
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HPDK1
 
Molecule 2 - SERINE/THREONINE-PROTEIN KINASE N2
    Chains: B
    Engineered: YES
    Fragment: PIFTIDE (PRK2 HYDROPHOBIC MOTIF, UNP RESIDUES 969-983)
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PKN GAMMA, PROTEIN KINASE C-LIKE 2, PROTEIN-KINASE C-RELATED KINASE 2
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2GOL2Ligand/IonGLYCEROL
3SEP1Mod. Amino AcidPHOSPHOSERINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
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:2083 , HOH A:2096 , HOH A:2098 , HOH A:2152 , HOH A:2184 , HOH A:2193 , HOH A:2247 , HOH A:2263BINDING SITE FOR RESIDUE ATP A 401
2AC2SOFTWAREALA A:103 , THR A:104 , HIS A:139 , SER A:191 , TRP A:347 , ASN A:349 , LEU A:350 , HIS A:351 , HOH A:2015 , HOH A:2070BINDING SITE FOR RESIDUE GOL A 402
3AC3SOFTWARELYS A:83 , PHE A:84 , GLU A:194 , GLY A:334 , LYS A:337BINDING SITE FOR RESIDUE GOL A 403

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4RRV)

(-) 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:284
                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhh.eeeeeeeee....eeeeeee.....eeeeeeeehhhhhhh.hhhhhhhhhhhhh.........eeeeee...eeeeee.....eehhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee...............hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh.........hhhhhhhhhhhh..hhhhh..hhhhhhhhhhhhhhhhh.....hhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rrv A  76 KKRPEDFKFGKILGEGSFSTVVLARELATSREYAIKILEKRHIIKENKVPYVTRERDVMSRLDHPFFVKLYFTFQDDEKLYFGLSYAKNGELLKYIRKIGSFDETCTRFYTAEIVSALEYLHGKGIIHRDLKPENILLNEDMHIQITDFGTAKVLSPESKQARANsFVGTAQYVSPELLTEKSACKSSDLWALGCIIYQLVAGLPPFRAGNEGLIFAKIIKLEYDFPEKFFPKARDLVEKLLVLDATKRLGCEEMEGYGPLKAHPFFESVTWENLHQQTPPKLT 359
                                    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    
                                                                                                                                                                                               241-SEP                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ......ee. Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 4rrv B  13 MFRDFDYIA  21
   Legend:   → Mismatch (orange background)
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    → 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 4RRV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (79, 100)

Asymmetric/Biological Unit(hide GO term definitions)

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  PDPK1_HUMAN | O15530
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  PKN2_HUMAN | Q16513
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  2.7.11.1
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 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 4xx9 5ack 5hkm 5hng 5ho7 5ho8 5lvl 5lvm 5lvn 5lvo 5lvp 5mrd
        PKN2_HUMAN | Q16513: 4crs

(-) Related Entries Specified in the PDB File

4rqk PDK1 IN COMPLEX WITH ATP AND THE PIF-POCKET LIGAND RS1
4rqv PDK1 IN COMPLEX WITH ATP AND THE PIF-POCKET LIGAND RS2