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(-) Description

Title :  HUMAN PDK1-PKCIOTA KINASE CHIMERA IN COMPLEX WITH ALLOSTERIC COMPOUND PS267 BOUND TO THE PIF-POCKET
 
Authors :  J. M. Arencibia, W. Froehner, M. Krupa, D. Pastor-Flores, P. Merker, T. Oellerich, S. Neimanis, C. Schmithals, V. Koeberle, E. Suess, S. Ze H. Stark, A. Piiper, D. Odadzic, J. O. Schulze, R. M. Biondi
Date :  22 Dec 16  (Deposition) - 18 Jan 17  (Release) - 01 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.41
Chains :  Asym./Biol. Unit :  A
Keywords :  Protein Kinase, Allosteric Regulation, Small Compounds, Pif-Pocket, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. M. Arencibia, W. Frohner, M. Krupa, D. Pastor-Flores, P. Merker, T. Oellerich, S. Neimanis, C. Schmithals, V. Koberle, E. Su, S. Zeuzem H. Stark, A. Piiper, D. Odadzic, J. O. Schulze, R. M. Biondi
An Allosteric Inhibitor Scaffold Targeting The Pif-Pocket O Atypical Protein Kinase C Isoforms.
Acs Chem. Biol. V. 12 564 2017
PubMed-ID: 28045490  |  Reference-DOI: 10.1021/ACSCHEMBIO.6B00827

(-) 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 Taxid: 7108
    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  (5, 6)

Asymmetric/Biological Unit (5, 6)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2DMS2Ligand/IonDIMETHYL SULFOXIDE
3DTT1Ligand/Ion2,3-DIHYDROXY-1,4-DITHIOBUTANE
4S261Ligand/IonETHYL (2~{S})-1-(6-CHLORANYL-1,3-BENZOTHIAZOL-2-YL)-4-OXIDANYL-5-OXIDANYLIDENE-2-THIOPHEN-2-YL-2~{H}-PYRROLE-3-CARBOXYLATE
5SEP1Mod. Amino AcidPHOSPHOSERINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:118 , ASN A:119 , ILE A:124 , GLN A:128 , LYS A:131 , GLN A:150 , LEU A:155 , HOH A:557binding site for residue S26 A 401
2AC2SOFTWAREGLY A:244 , ALA A:246 , ARG A:283 , GLU A:287 , ASP A:300 , PRO A:302 , HOH A:666binding site for residue DTT A 402
3AC3SOFTWARETHR A:104 , SER A:105 , HIS A:139 , TRP A:347 , GLU A:348 , ASN A:349 , LEU A:350 , HIS A:351 , HOH A:604binding site for residue DMS A 403
4AC4SOFTWAREPRO A:79 , PHE A:82 , PHE A:84binding site for residue DMS A 404
5AC5SOFTWARELEU A:88 , GLY A:89 , SER A:94 , VAL A:96 , LYS A:111 , TYR A:126 , SER A:160 , ALA A:162 , GLU A:166 , LEU A:212 , ASP A:223 , HOH A:519 , HOH A:556 , HOH A:693binding site for residue ATP A 405

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5MRD)

(-) 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...eeeeeeee.....eeeeeeeehhhhhhh.hhhhhhhhhhhhhhh.......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
                 5mrd A  76 SKRPEDFKFGKILGEGSFSTVVLARELATSREYAIKIVEKRHVNKENKIPYVQREKDVMSRLDHPFFVKLYFCFQDDEKLYFGLSYAKNGELLKYIRKIGSFDETCTRFYTAEIVSALEYLHGKGIIHRDLKPENILLNEDMHIQITDFGTAKVLSPESKQARANsFVGTAQYVSPELLTEKSACKSSDLWALGCIIYQLVAGLPPFRAGNEGLIFAKIIKLEYDFPEKFFPKARDLVEKLLVLDATKRLGCEEMEGYGPLKAHPFFESVTWENLHQQTPPKLT 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
   Legend:   → Mismatch (orange background)
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  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 5MRD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (56, 56)

Asymmetric/Biological Unit(hide GO term definitions)

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  5mrd
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  PDPK1_HUMAN | O15530
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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 4rrv 4xx9 5ack 5hkm 5hng 5ho7 5ho8 5lvl 5lvm 5lvn 5lvo 5lvp

(-) Related Entries Specified in the PDB File

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