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(-) Description

Title :  CRYSTAL STRUCTURE OF PYRUVATE DEHYDROGENASE KINASE ISOFORM 2 IN COMPLEX WITH INHIBITOR PS2
 
Authors :  W. J. Gui, S. C. Tso, J. L. Chuang, C. Y. Wu, X. Qi, U. K. Tambar, R. M. Wynn, D
Date :  12 Sep 13  (Deposition) - 01 Jan 14  (Release) - 05 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Ghkl Protein Kinase, Pyruvate Dehydrogenase Complex, Mitochondrial Protein Kinases, Impaired Glucose Oxidation, Hepatic Steatosis, Type 2 Diabetes, Cancer, Bergerat Nucleotide-Binding Fold, Protein Kinase, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. C. Tso, X. Qi, W. J. Gui, C. Y. Wu, J. L. Chuang, I. Wernstedt-Asterholm, L. K. Morlock, K. R. Owens, P. E. Scherer, N. S. Williams, U. K. Tambar, R. M. Wynn, D. T. Chuang
Structure-Guided Development Of Specific Pyruvate Dehydrogenase Kinase Inhibitors Targeting The Atp-Binding Pocket.
J. Biol. Chem. V. 289 4432 2014
PubMed-ID: 24356970  |  Reference-DOI: 10.1074/JBC.M113.533885

(-) Compounds

Molecule 1 - [PYRUVATE DEHYDROGENASE [LIPOAMIDE]] KINASE ISOZYME 2, MITOCHONDRIAL
    Chains: A
    EC Number: 2.7.11.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 511693
    Gene: PDK2, PDHK2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PYRUVATE DEHYDROGENASE KINASE ISOFORM 2, PDH KINASE 2, PDKII

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1PV21Ligand/Ion4-(ISOINDOLIN-2-YLSULFONYL)BENZENE-1,3-DIOL
2TLA1Ligand/IonL(+)-TARTARIC ACID
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1PV22Ligand/Ion4-(ISOINDOLIN-2-YLSULFONYL)BENZENE-1,3-DIOL
2TLA2Ligand/IonL(+)-TARTARIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:262 , SER A:263 , HIS A:264 , GLU A:265 , SER A:266BINDING SITE FOR RESIDUE TLA A 501
2AC2SOFTWARELEU A:252 , ASN A:255 , ARG A:258 , ALA A:259 , GLU A:262 , ASP A:290 , GLY A:294 , VAL A:295 , THR A:354 , HOH A:602 , HOH A:604 , HOH A:746BINDING SITE FOR RESIDUE PV2 A 502

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4MPC)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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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:363
                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains d4mpca1 A:12-177 automated matches                                                                                                                                    d4mpca2 A:182-394 automated matches                                                                                                                                                                   SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh.......hhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........eeeeehhhhhhhhhhhhhhhhhhhhh....eeeeeee........eeeehhhhhhhhhhhhhhhhhhhhhhh.........eeeeeee...eeeeeeee.....hhhhhhhhhh......hhhhhhhhhhhhh..eeeeeee...eeeeeeeee.............hhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mpc A  12 SLAGAPKYIEHFSKFSPSPLSMKQFLDFGSSNACEKTSFTFLRQELPVRLANIMKEINLLPDRVLSTPSVQLVQSWYVQSLLDIMEFLDKDPEDHRTLSQFTDALVTIRNRHNDVVPTMAQGVLEYKDTYGDDPVSNQNIQYFLDRFYLSRISIRMLINQHTLIFDPAHPKHIGSIDPNCNVSEVVKDAYDMAKLLCDKYYMASPDLEIQEINAANSKQPIHMVYVPSHLYHMLFELFKNAMRATVESHESSLILPPIKVMVALGEEDLSIKMSDRGGGVPLRKIERLFSYMYSTGYGLPISRLYAKYFQGDLQLFSMEGFGTDAVIYLKALSTDSVERLPVYNKSAWRHYQTIQEAGDWCVP 394
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171     ||185       195       205       215       225       235       245       255       265       275       285       295       305    || 331       341       351       361       371       381       391   
                                                                                                                                                                                               177|                                                                                                                             310|                                                                   
                                                                                                                                                                                                182                                                                                                                              327
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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  (2, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (26, 26)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PDK2_HUMAN | Q15119: 2btz 2bu2 2bu5 2bu6 2bu7 2bu8 4mp2 4mp7 4mpe 4mpn 4v25 4v26 5j6a 5j71 5m4k 5m4m 5m4n 5m4p

(-) Related Entries Specified in the PDB File

4mp2 THE SAME PROTEIN WITH DIFFERENT INHIBITOR
4mp7 THE SAME PROTEIN WITH DIFFERENT INHIBITOR
4mpe THE SAME PROTEIN WITH DIFFERENT INHIBITOR