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(-) Description

Title :  HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH AN HM-PEPTIDE 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 :  2.50
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,F  (1x)
Biol. Unit 2:  B,G  (1x)
Biol. Unit 3:  C,E  (1x)
Biol. Unit 4:  D,H  (1x)
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, B, C, D
    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
 
Molecule 2 - HYDROPHOBIC-MOTIF PEPTIDE OF PKB/AKT
    Chains: E, F, G, H
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): A    F  
Biological Unit 2 (1x):  B    G 
Biological Unit 3 (1x):   C E   
Biological Unit 4 (1x):    D   H

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 14)

Asymmetric Unit (3, 14)
No.NameCountTypeFull Name
1ATP4Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2CL2Ligand/IonCHLORIDE ION
3SEP8Mod. Amino AcidPHOSPHOSERINE
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2CL-1Ligand/IonCHLORIDE ION
3SEP2Mod. Amino AcidPHOSPHOSERINE
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2CL-1Ligand/IonCHLORIDE ION
3SEP2Mod. Amino AcidPHOSPHOSERINE
Biological Unit 3 (2, 3)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2CL-1Ligand/IonCHLORIDE ION
3SEP2Mod. Amino AcidPHOSPHOSERINE
Biological Unit 4 (2, 3)
No.NameCountTypeFull Name
1ATP1Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2CL-1Ligand/IonCHLORIDE ION
3SEP2Mod. Amino AcidPHOSPHOSERINE

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY 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:609binding site for residue ATP A 500
02AC2SOFTWAREGLY B:89 , GLY B:91 , SER B:92 , SER B:94 , VAL B:96 , ALA B:109 , LYS B:111 , SER B:160 , ALA B:162 , GLU B:166 , LEU B:212 , HOH B:519 , HOH B:536 , HOH B:549binding site for residue ATP B 401
03AC3SOFTWAREGLY C:89 , GLY C:91 , SER C:92 , SER C:94 , VAL C:96 , ALA C:109 , LYS C:111 , SER C:160 , ALA C:162 , GLU C:166 , GLU C:209 , LEU C:212 , HOH C:504 , HOH C:508 , HOH C:537binding site for residue ATP C 401
04AC4SOFTWARELYS C:144binding site for residue CL C 402
05AC5SOFTWAREGLY D:89 , GLU D:90 , GLY D:91 , SER D:92 , SER D:94 , VAL D:96 , ALA D:109 , LYS D:111 , SER D:160 , ALA D:162 , GLU D:166 , LEU D:212binding site for residue ATP D 500
06AC6SOFTWAREARG C:131 , THR C:148 , PHE C:149 , GLN C:150 , PHE E:8 , PRO E:9 , GLN E:10 , TYR E:13binding site for Di-peptide PHE E 11 and SEP E 12
07AC7SOFTWARELEU C:145 , PHE C:147 , THR C:148 , GLN C:150 , PHE E:8 , GLN E:10 , PHE E:11 , SER E:14binding site for Di-peptide SEP E 12 and TYR E 13
08AC8SOFTWAREARG A:131 , THR A:148 , PHE A:149 , GLN A:150 , PHE A:157 , PHE F:8 , PRO F:9 , GLN F:10 , TYR F:13binding site for Di-peptide PHE F 11 and SEP F 12
09AC9SOFTWARESER A:135 , PHE A:147 , THR A:148 , GLN A:150 , PRO F:9 , GLN F:10 , PHE F:11 , SER F:14binding site for Di-peptide SEP F 12 and TYR F 13
10AD1SOFTWAREARG B:131 , THR B:148 , GLN B:150 , PHE B:157 , HOH B:547 , PHE G:8 , PRO G:9 , GLN G:10 , TYR G:13binding site for Di-peptide PHE G 11 and SEP G 12
11AD2SOFTWAREPHE B:147 , THR B:148 , GLN B:150 , HOH B:547 , PRO G:9 , GLN G:10 , PHE G:11 , SER G:14binding site for Di-peptide SEP G 12 and TYR G 13
12AD3SOFTWAREARG D:131 , THR D:148 , PHE D:149 , GLN D:150 , LEU D:155 , PHE D:157 , PHE H:8 , PRO H:9 , GLN H:10 , TYR H:13binding site for Di-peptide PHE H 11 and SEP H 12
13AD4SOFTWARESER D:135 , LEU D:145 , THR D:148 , GLN D:150 , GLN H:10 , PHE H:11 , SER H:14binding site for Di-peptide SEP H 12 and TYR H 13

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5LVP)

(-) Sequences/Alignments

Asymmetric 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:276
                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhh.eeeeeeeeee..eeeeeeee.....eeeeeeeehhhhhhh.hhhhhhhhhhhhhh........eeeeee...eeeeee......hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee......hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh........hhhhhhhhhh...........hhhhhhhhhhhhhhhhh..hhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5lvp A  75 RKKRPEDFKFGKILGEGSFSTVVLARELATSREYAIKILEKRHIIKENKVPYVTRERDVMSRLDHPFFVKLYFTFQDDEKLYFGLSYAKNGELLKYIRKIGSFDETCTRFYTAEIVSALEYLHGKGIIHRDLKPENILLNEDMHIQITDFGTAKVLNsFVGTAQYVSPELLTEKSACKSSDLWALGCIIYQLVAGLPPFRAGNEGLIFAKIIKLEYDFPEKFFPKARDLVEKLLVLDATKRLGCEEMEGYGPLKAHPFFESVTWENLHQQTPPKLT 359
                                    84        94       104       114       124       134       144       154       164       174       184       194       204       214       224     ||243       253       263       273       283       293       303       313       323       333       343       353      
                                                                                                                                                                                     230||                                                                                                                      
                                                                                                                                                                                      240|                                                                                                                      
                                                                                                                                                                                       241-SEP                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:277
                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhh.eeeeeeee.....eeeeeee.....eeeeeeeehhhhhh..hhhhhhhhhhhhhh........eeeeee...eeeeee......hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee......hhhhh..hhhhhh..hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh........hhhhhhhhhh....hhhhh..hhhhhhhhhhhhhhhhh.....hhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lvp B  74 PRKKRPEDFKFGKILGEGSFSTVVLARELATSREYAIKILEKRHIIKENKVPYVTRERDVMSRLDHPFFVKLYFTFQDDEKLYFGLSYAKNGELLKYIRKIGSFDETCTRFYTAEIVSALEYLHGKGIIHRDLKPENILLNEDMHIQITDFGTAKVLSsFVGTAQYVSPELLTEKSACKSSDLWALGCIIYQLVAGLPPFRAGNEGLIFAKIIKLEYDFPEKFFPKARDLVEKLLVLDATKRLGCEEMEGYGPLKAHPFFESVTWENLHQQTPPKLT 359
                                    83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       242       252       262       272       282       292       302       312       322       332       342       352       
                                                                                                                                                                                       231|                                                                                                                      
                                                                                                                                                                                        241-SEP                                                                                                                  


Chain C from PDB  Type:PROTEIN  Length:276
                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhh.eeeeeeee....eeeeeeee.....eeeeeeeehhhhhhh.hhhhhhhhhhhhhh........eeeeee...eeeeee......hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee......hhhhh..hhhhhh..hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh.........hhhhhhhhhhhh..hhhhh..hhhhhhhhhhhhhhhhh..hhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5lvp C  75 RKKRPEDFKFGKILGEGSFSTVVLARELATSREYAIKILEKRHIIKENKVPYVTRERDVMSRLDHPFFVKLYFTFQDDEKLYFGLSYAKNGELLKYIRKIGSFDETCTRFYTAEIVSALEYLHGKGIIHRDLKPENILLNEDMHIQITDFGTAKVLNsFVGTAQYVSPELLTEKSACKSSDLWALGCIIYQLVAGLPPFRAGNEGLIFAKIIKLEYDFPEKFFPKARDLVEKLLVLDATKRLGCEEMEGYGPLKAHPFFESVTWENLHQQTPPKLT 359
                                    84        94       104       114       124       134       144       154       164       174       184       194       204       214       224     ||243       253       263       273       283       293       303       313       323       333       343       353      
                                                                                                                                                                                     230||                                                                                                                      
                                                                                                                                                                                      240|                                                                                                                      
                                                                                                                                                                                       241-SEP                                                                                                                  


Chain D from PDB  Type:PROTEIN  Length:277
                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhh.eeeeeeeeee..eeeeeeee.....eeeeeeeehhhhhhh.hhhhhhhhhhhhhh........eeeeee...eeeeee......hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee........eee.....eee......ee......hhhhh..hhhhhh..hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh.........hhhhhhhhhhhh..hhhhh..hhhhhhhhhhhhhhhhh..hhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5lvp D  74 PRKKRPEDFKFGKILGEGSFSTVVLARELATSREYAIKILEKRHIIKENKVPYVTRERDVMSRLDHPFFVKLYFTFQDDEKLYFGLSYAKNGELLKYIRKIGSFDETCTRFYTAEIVSALEYLHGKGIIHRDLKPENILLNEDMHIQITDFGTAKVLNsFVGTAQYVSPELLTEKSACKSSDLWALGCIIYQLVAGLPPFRAGNEGLIFAKIIKLEYDFPEKFFPKARDLVEKLLVLDATKRLGCEEMEGYGPLKAHPFFESVTWENLHQQTPPKLT 359
                                    83        93       103       113       123       133       143       153       163       173       183       193       203       213       223      |242       252       262       272       282       292       302       312       322       332       342       352       
                                                                                                                                                                                      230||                                                                                                                      
                                                                                                                                                                                       240|                                                                                                                      
                                                                                                                                                                                        241-SEP                                                                                                                  


Chain E from PDB  Type:PROTEIN  Length:7
                                       
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ....... Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                 5lvp E   8 FPQFsYS  14
                                |  
                               12-SEP


Chain F from PDB  Type:PROTEIN  Length:8
                                        
               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
                 5lvp F   8 FPQFsYSA  15
                                |   
                               12-SEP


Chain G from PDB  Type:PROTEIN  Length:8
                                        
               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
                 5lvp G   8 FPQFsYSA  15
                                |   
                               12-SEP


Chain H from PDB  Type:PROTEIN  Length:7
                                       
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ....... Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                 5lvp H   8 FPQFsYS  14
                                |  
                               12-SEP
   Legend:   → Mismatch (orange background)
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  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 5LVP)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (56, 56)

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  5lvp
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  PDPK1_HUMAN | O15530
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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 5mrd

(-) Related Entries Specified in the PDB File

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