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(-) Description

Title :  INHIBITOR-BOUND STRUCTURES OF HUMAN PYRUVATE DEHYDROGENASE KINASE 4
 
Authors :  M. Kawamoto, I. Shiromizu, M. Kukimoto-Niino, A. Tokmakov, T. Terada, M. Shirouzu, T. Matsusue, S. Yokoyama
Date :  01 Dec 07  (Deposition) - 09 Dec 08  (Release) - 23 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Pdk4, Kinase, Atp-Binding, Adp, Carbohydrate Metabolism, Glucose Metabolism, Mitochondrion, Phosphoprotein, Transferase, Transit Peptide (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Kukimoto-Niino, A. Tokmakov, T. Terada, N. Ohbayashi, T. Fujimoto S. Gomi, I. Shiromizu, M. Kawamoto, T. Matsusue, M. Shirouzu, S. Yokoyama
Inhibitor-Bound Structures Of Human Pyruvate Dehydrogenase Kinase 4.
Acta Crystallogr. , Sect. D V. 67 763 2011
PubMed-ID: 21904029  |  Reference-DOI: 10.1107/S090744491102405X

(-) Compounds

Molecule 1 - PYRUVATE DEHYDROGENASE KINASE ISOZYME 4
    ChainsA, B
    EC Number2.7.11.2
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System Cell LineSF9
    Expression System CommonFALL ARMYWORM
    Expression System Taxid7108
    Expression System VectorPBLUEBAC4.5
    Expression System Vector TypeBACULOVIRUS
    FragmentRESIDUES 20-411
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPYRUVATE DEHYDROGENASE KINASE ISOFORM 4

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2EPE1Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
3MG2Ligand/IonMAGNESIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:254 , ASN A:258 , ADP A:501 , HOH A:676BINDING SITE FOR RESIDUE MG A 500
2AC2SOFTWAREGLU B:254 , ASN B:258 , ADP B:1501BINDING SITE FOR RESIDUE MG B1500
3AC3SOFTWAREASN A:258 , ARG A:261 , ALA A:262 , ASP A:293 , VAL A:298 , LEU A:306 , SER A:312 , THR A:313 , ALA A:328 , GLY A:329 , PHE A:330 , GLY A:331 , GLY A:333 , LEU A:334 , THR A:358 , MG A:500 , HOH A:602 , HOH A:604 , HOH A:676BINDING SITE FOR RESIDUE ADP A 501
4AC4SOFTWAREASN B:258 , ARG B:261 , ALA B:262 , ASP B:293 , VAL B:298 , LEU B:306 , SER B:312 , THR B:313 , GLY B:329 , PHE B:330 , GLY B:331 , GLY B:333 , LEU B:334 , THR B:358 , MG B:1500 , HOH B:1503 , HOH B:1510BINDING SITE FOR RESIDUE ADP B1501
5AC5SOFTWAREASP A:160 , ARG A:338 , LYS A:342 , LYS A:374 , TRP B:395BINDING SITE FOR RESIDUE EPE A 600

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2ZDY)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2ZDY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 3)

Asymmetric/Biological Unit (2, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_042299L19MPDK4_HUMANPolymorphism55761955AP19M
2UniProtVAR_042300D109GPDK4_HUMANPolymorphism34898343A/BD109G

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2ZDY)

(-) Exons   (11, 22)

Asymmetric/Biological Unit (11, 22)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000000051781aENSE00001133344chr7:95225803-95225476328PDK4_HUMAN1-44442A:19-44
B:21-44
26
24
1.2aENST000000051782aENSE00000706270chr7:95224476-95224335142PDK4_HUMAN44-91482A:44-91 (gaps)
B:44-91
48
48
1.3ENST000000051783ENSE00000706269chr7:95223082-9522301172PDK4_HUMAN91-115252A:91-115
B:91-115
25
25
1.4aENST000000051784aENSE00000706268chr7:95222256-95222072185PDK4_HUMAN115-177632A:115-177 (gaps)
B:115-177
63
63
1.4cENST000000051784cENSE00000706266chr7:95221909-9522182387PDK4_HUMAN177-206302A:177-206
B:177-206 (gaps)
30
30
1.5ENST000000051785ENSE00000706265chr7:95221377-9522130078PDK4_HUMAN206-232272A:206-232
B:206-232
27
27
1.6bENST000000051786bENSE00000706264chr7:95219028-9521895277PDK4_HUMAN232-257262A:232-257
B:232-257
26
26
1.7aENST000000051787aENSE00000706262chr7:95217137-9521703999PDK4_HUMAN258-290332A:258-290
B:258-290
33
33
1.7dENST000000051787dENSE00000706260chr7:95216840-95216730111PDK4_HUMAN291-327372A:291-327 (gaps)
B:291-313
37
23
1.8aENST000000051788aENSE00000706258chr7:95216435-95216322114PDK4_HUMAN328-365382A:328-365
B:329-365
38
37
1.9bENST000000051789bENSE00001267271chr7:95215093-952128112283PDK4_HUMAN366-411462A:366-386
B:366-398 (gaps)
21
33

(-) 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:354
 aligned with PDK4_HUMAN | Q16654 from UniProtKB/Swiss-Prot  Length:411

    Alignment length:368
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378        
           PDK4_HUMAN    19 LVPREVEHFSRYSPSPLSMKQLLDFGSENACERTSFAFLRQELPVRLANILKEIDILPTQLVNTSSVQLVKSWYIQSLMDLVEFHEKSPDDQKALSDFVDTLIKVRNRHHNVVPTMAQGIIEYKDACTVDPVTNQNLQYFLDRFYMNRISTRMLMNQHILIFSDSQTGNPSHIGSIDPNCDVVAVVQDAFECSRMLCDQYYLSSPELKLTQVNGKFPDQPIHIVYVPSHLHHMLFELFKNAMRATVEHQENQPSLTPIEVIVVLGKEDLTIKISDRGGGVPLRIIDRLFSYTYSTAPTPVMDNSRNAPLAGFGYGLPISRLYAKYFQGDLNLYSLSGYGTDAIIYLKALSSESIEKLPVFNKSAFKHY 386
               SCOP domains d2zdya1 A:19-187 automated    matches                                                                                                                                    d2zdya2 A:188-386 automated matches                                                                                                                                                                     SCOP domains
               CATH domains 2zdyA01 A:19-189  [code=1.2   0.140.20, no name defined]                                                                                                                   2zdyA02 A:190-374  [code=3.30.565.10, no name defined]                                                                                                                                   ------------ CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhh.......hhhhhhhh..---hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh---......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............eeeeehhhhhhhhhhhhhhhhhhhhh....eeeeeee........eeeehhhhhhhhhhhhhhhhhhhhhhhh........eeeeeee...eeeeeee......hhhhhhhhh..........--------......hhhhhhhhhhhhh..eeeeeee...eeeeeeeee.hhhhh.......hhhhhhhh Sec.struct. author
                 SAPs(SNPs) M-----------------------------------------------------------------------------------------G------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: A:19-44   ----------------------------------------------Exon 1.3  PDB: A:91-115  -------------------------------------------------------------Exon 1.4c  PDB: A:177-206     -------------------------Exon 1.6b  PDB: A:232-257 Exon 1.7a  PDB: A:258-290        Exon 1.7d  PDB: A:291-327 (gaps)     Exon 1.8a  PDB: A:328-365             Exon 1.9b             Transcript 1 (1)
           Transcript 1 (2) -------------------------Exon 1.2a  PDB: A:44-91 (gaps) UniProt: 44-91   -----------------------Exon 1.4a  PDB: A:115-177 (gaps) UniProt: 115-177              ----------------------------Exon 1.5  PDB: A:206-232   ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2zdy A  19 PVPREVEHFSRYSPSPLSMKQLLDFGS---CERTSFAFLRQELPVRLANILKEIDILPTQLVNTSSVQLVKSWYIQSLMDLVEFHEKSPDDQKALSDFVDTLIKVRNRHHNVVPTMAQGIIEYK---TVDPVTNQNLQYFLDRFYMNRISTRMLMNQHILIFSDSQTGNPSHIGSIDPNCDVVAVVQDAFECSRMLCDQYYLSSPELKLTQVNGKFPDQPIHIVYVPSHLHHMLFELFKNAMRATVEHQENQPSLTPIEVIVVLGKEDLTIKISDRGGGVPLRIIDRLFSYTYSTAPTP--------PLAGFGYGLPISRLYAKYFQGDLNLYSLSGYGTDAIIYLKALSSESIEKLPVFNKSAFKHY 386
                                    28        38      |  -|       58        68        78        88        98       108       118       128       138   |   148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308        |-       328       338       348       358       368       378        
                                                     45  49                                                                                          142 146                                                                                                                                                                        317      326                                                            

Chain B from PDB  Type:PROTEIN  Length:354
 aligned with PDK4_HUMAN | Q16654 from UniProtKB/Swiss-Prot  Length:411

    Alignment length:378
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390        
           PDK4_HUMAN    21 PREVEHFSRYSPSPLSMKQLLDFGSENACERTSFAFLRQELPVRLANILKEIDILPTQLVNTSSVQLVKSWYIQSLMDLVEFHEKSPDDQKALSDFVDTLIKVRNRHHNVVPTMAQGIIEYKDACTVDPVTNQNLQYFLDRFYMNRISTRMLMNQHILIFSDSQTGNPSHIGSIDPNCDVVAVVQDAFECSRMLCDQYYLSSPELKLTQVNGKFPDQPIHIVYVPSHLHHMLFELFKNAMRATVEHQENQPSLTPIEVIVVLGKEDLTIKISDRGGGVPLRIIDRLFSYTYSTAPTPVMDNSRNAPLAGFGYGLPISRLYAKYFQGDLNLYSLSGYGTDAIIYLKALSSESIEKLPVFNKSAFKHYQMSSEADDWCIP 398
               SCOP domains d2zdyb1 B:21-187 automated matches                                                                                                                                     d2zdyb2 B:188-398 automated matches                                                                                                                                                                                 SCOP domains
               CATH domains 2zdyB01 B:21-189  [code=1.20.140.20, no name defined]                                                                                                                    2zdyB02 B:190-374  [code=3.30.565.10, no name defined]                                                                                                                                   ------------      ------ CATH domains
           Pfam domains (1) ------------BCDHK_Adom3-2zdyB03 B:33-196                                                                                                                                        ----------------------------------------------HATPase_c-2zdyB01 B:243-367                                                                                                  -------------------      ------ Pfam domains (1)
           Pfam domains (2) ------------BCDHK_Adom3-2zdyB04 B:33-196                                                                                                                                        ----------------------------------------------HATPase_c-2zdyB02 B:243-367                                                                                                  -------------------      ------ Pfam domains (2)
         Sec.struct. author hhhhhhhh.......hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh---..........eeeeehhhhhhhhhhhhhhhhhhhhh....eeeeeee........eeeehhhhhhhhhhhhhhhhhhhhhhhh........eeeeeee...eeeeeeee........hhhhhh......---------------...hhhhhhhhhhhhh..eeeeeee...eeeeeeeee.............hhhhhhhh------...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------G------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: B:21-44 ----------------------------------------------Exon 1.3  PDB: B:91-115  -------------------------------------------------------------Exon 1.4c UniProt: 177-206    -------------------------Exon 1.6b  PDB: B:232-257 Exon 1.7a  PDB: B:258-290        Exon 1.7d  PDB: B:291-313            Exon 1.8a  PDB: B:329-365 [INCOMPLETE]Exon 1.9b  PDB: B:366-398 (gaps)  Transcript 1 (1)
           Transcript 1 (2) -----------------------Exon 1.2a  PDB: B:44-91 UniProt: 44-91          -----------------------Exon 1.4a  PDB: B:115-177 UniProt: 115-177                     ----------------------------Exon 1.5  PDB: B:206-232   ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2zdy B  21 PREVEHFSRYSPSPLSMKQLLDFGSENACERTSFAFLRQELPVRLANILKEIDILPTQLVNTSSVQLVKSWYIQSLMDLVEFHEKSPDDQKALSDFVDTLIKVRNRHHNVVPTMAQGIIEYKDACTVDPVTNQNLQYFLDRFYMNRISTRMLMNQHILIFS---TGNPSHIGSIDPNCDVVAVVQDAFECSRMLCDQYYLSSPELKLTQVNGKFPDQPIHIVYVPSHLHHMLFELFKNAMRATVEHQENQPSLTPIEVIVVLGKEDLTIKISDRGGGVPLRIIDRLFSYTYST---------------GFGYGLPISRLYAKYFQGDLNLYSLSGYGTDAIIYLKALSSESIEKLPVFNKSAFKHY------DDWCIP 398
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180|   |  190       200       210       220       230       240       250       260       270       280       290       300       310  |      -       330       340       350       360       370       380     |   -  |     
                                                                                                                                                                                          181 185                                                                                                                             313             329                                                      386    393     

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → 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  (2, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit

(-) Gene Ontology  (29, 29)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PDK4_HUMAN | Q16654)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
    GO:0004740    pyruvate dehydrogenase (acetyl-transferring) kinase activity    Catalysis of the reaction: ATP + pyruvate dehydrogenase (acetyl-transferring) = ADP + pyruvate dehydrogenase (acetyl-transferring) phosphate.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0071398    cellular response to fatty acid    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a fatty acid stimulus.
    GO:0009267    cellular response to starvation    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of deprivation of nourishment.
    GO:0042593    glucose homeostasis    Any process involved in the maintenance of an internal steady state of glucose within an organism or cell.
    GO:0006006    glucose metabolic process    The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides.
    GO:0008286    insulin receptor signaling pathway    The series of molecular signals generated as a consequence of the insulin receptor binding to insulin.
    GO:2000811    negative regulation of anoikis    Any process that stops, prevents or reduces the frequency, rate or extent of anoikis.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0002230    positive regulation of defense response to virus by host    Any host process that results in the promotion of antiviral immune response mechanisms, thereby limiting viral replication.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0072593    reactive oxygen species metabolic process    The chemical reactions and pathways involving a reactive oxygen species, any molecules or ions formed by the incomplete one-electron reduction of oxygen. They contribute to the microbicidal activity of phagocytes, regulation of signal transduction and gene expression, and the oxidative damage to biopolymers.
    GO:0010510    regulation of acetyl-CoA biosynthetic process from pyruvate    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of acetyl-CoA from pyruvate.
    GO:0045124    regulation of bone resorption    Any process that modulates the frequency, rate or extent of bone tissue loss (resorption).
    GO:0010565    regulation of cellular ketone metabolic process    Any process that modulates the chemical reactions and pathways involving any of a class of organic compounds that contain the carbonyl group, CO, and in which the carbonyl group is bonded only to carbon atoms. The general formula for a ketone is RCOR, where R and R are alkyl or aryl groups.
    GO:0042304    regulation of fatty acid biosynthetic process    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of fatty acids, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils.
    GO:0046320    regulation of fatty acid oxidation    Any process that modulates the frequency, rate or extent of fatty acid oxidation.
    GO:0010906    regulation of glucose metabolic process    Any process that modulates the rate, frequency or extent of glucose metabolism. Glucose metabolic processes are the chemical reactions and pathways involving glucose, the aldohexose gluco-hexose.
    GO:0006885    regulation of pH    Any process involved in the maintenance of an internal equilibrium of hydrogen ions, thereby modulating the internal pH, within an organism or cell.
    GO:0042594    response to starvation    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a starvation stimulus, deprivation of nourishment.
    GO:0098792    xenophagy    The macroautophagy process in which a region of cytoplasm containing an intracellular pathogen or some part of an intracellular pathogen (e.g. viral capsid) is enclosed in a double membrane bound autophagosome, which then fuses with the lysosome leading to degradation of the contents.
cellular component
    GO:0005743    mitochondrial inner membrane    The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
    GO:0005759    mitochondrial matrix    The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PDK4_HUMAN | Q166542e0a 2zdx 2zkj 3d2r

(-) Related Entries Specified in the PDB File

2zdx