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(-) Description

Title :  HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH ALLOSTERIC COMPOUND PSE10 BOUND TO THE PIF-POCKET
 
Authors :  J. O. Schulze, G. Saladino, K. Busschots, S. Neimanis, E. Suess, D. Odad S. Zeuzem, V. Hindie, A. K. Herbrand, M. N. Lisa, P. M. Alzari, F. L. Gerv R. M. Biondi
Date :  14 Sep 16  (Deposition) - 19 Oct 16  (Release) - 02 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.09
Chains :  Asym./Biol. Unit :  A
Keywords :  Protein Kinase, Allosteric Regulation, Small Compounds, Pif-Pocket, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. O. Schulze, G. Saladino, K. Busschots, S. Neimanis, E. Su, D. Odadzic, S. Zeuzem, V. Hindie, A. K. Herbrand, M. N. Lisa, P. M. Alzari, F. L. Gervasio, R. M. Biondi
Bidirectional Allosteric Communication Between The Atp-Binding Site And The Regulatory Pif Pocket In Pdk1 Protein Kinase.
Cell Chem Biol V. 23 1193 2016
PubMed-ID: 27693059  |  Reference-DOI: 10.1016/J.CHEMBIOL.2016.06.017

(-) 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  (6, 6)

Asymmetric/Biological Unit (6, 6)
No.NameCountTypeFull Name
178W1Ligand/Ion2-OXIDANYLIDENEPROPYL ~{N}-(2-CHLORANYL-6-FLUORANYL-PHENYL)CARBONYL-~{N}'-(4-CHLOROPHENYL)CARBAMIMIDOTHIOATE
2ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
3CL1Ligand/IonCHLORIDE ION
4DMS1Ligand/IonDIMETHYL SULFOXIDE
5DTD1Ligand/IonDITHIANE DIOL
6SEP1Mod. Amino AcidPHOSPHOSERINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
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:501 , HOH A:507 , HOH A:513 , HOH A:515 , HOH A:538 , HOH A:588 , HOH A:608 , HOH A:621 , HOH A:669 , HOH A:710 , HOH A:779binding site for residue ATP A 401
2AC2SOFTWAREILE A:119 , VAL A:127 , THR A:128 , THR A:148 , PHE A:149 , GLN A:150 , TYR A:156 , PHE A:157binding site for residue 78W 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:351binding site for residue DMS A 403
4AC4SOFTWAREPHE A:242 , VAL A:243 , GLY A:244 , THR A:245 , ALA A:246 , ARG A:283binding site for residue DTD A 404

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5LVO)

(-) 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    
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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:287
                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhh.eeeeeeeee....eeeeeee.....eeeeeeeehhhhhhh.hhhhhhhhhhhhhhh.......eeeeee...eeeeee.....eehhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee...............hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh.........hhhhhhhhhhhh..hhhhh..hhhhhhhhhhhhhhhhh..hhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lvo A  73 QPRKKRPEDFKFGKILGEGSFSTVVLARELATSREYAIKILEKRHIIKENKVPYVTRERDVMSRLDHPFFVKLYFTFQDDEKLYFGLSYAKNGELLKYIRKIGSFDETCTRFYTAEIVSALEYLHGKGIIHRDLKPENILLNEDMHIQITDFGTAKVLSPESKQARANsFVGTAQYVSPELLTEKSACKSSDLWALGCIIYQLVAGLPPFRAGNEGLIFAKIIKLEYDFPEKFFPKARDLVEKLLVLDATKRLGCEEMEGYGPLKAHPFFESVTWENLHQQTPPKLT 359
                                    82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       
                                                                                                                                                                                                  241-SEP
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5LVO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (56, 56)

Asymmetric/Biological Unit(hide GO term definitions)

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  5lvo
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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 5lvp 5mrd

(-) Related Entries Specified in the PDB File

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