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(-) Description

Title :  CRYSTAL STRUCTURE OF PYRUVATE DEHYDROGENASE KINASE ISOFORM 4 IN COMPLEX WITH ADP
 
Authors :  M. Kato, R. M. Wynn, L. C. Chuang, S. -C. Tso, J. Li, D. T. Chuang
Date :  08 May 08  (Deposition) - 05 Aug 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.03
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein-Nucleotide Complex, Homodimer, Ghkl Superfamily, Kinase, Carbohydrate Metabolism, Glucose Metabolism, Mitochondrion, Phosphoprotein, Transferase, Transit Peptide (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. M. Wynn, M. Kato, J. L. Chuang, S. C. Tso, J. Li, D. T. Chuang
Pyruvate Dehydrogenase Kinase-4 Structures Reveal A Metastable Open Conformation Fostering Robust Core-Free Basal Activity.
J. Biol. Chem. V. 283 25305 2008
PubMed-ID: 18658136  |  Reference-DOI: 10.1074/JBC.M802249200

(-) Compounds

Molecule 1 - [PYRUVATE DEHYDROGENASE [LIPOAMIDE]] KINASE ISOZYME 4
    ChainsA, B
    EC Number2.7.11.2
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21 (DE3)
    Expression System Vector TypePLASMID
    GenePDK4
    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, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2GOL2Ligand/IonGLYCEROL
3MG2Ligand/IonMAGNESIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:258BINDING SITE FOR RESIDUE MG A 500
2AC2SOFTWAREASN B:258BINDING SITE FOR RESIDUE MG B 500
3AC3SOFTWAREASN A:258 , ARG A:261 , ALA A:262 , ASP A:293 , LEU A:306 , TYR A:311 , 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:358BINDING SITE FOR RESIDUE ADP A 501
4AC4SOFTWAREASN B:258 , ARG B:261 , ALA B:262 , ASP B:293 , LEU B:306 , TYR B:311 , SER B:312 , THR B:313 , ALA B:328 , GLY B:329 , PHE B:330 , GLY B:331 , GLY B:333 , LEU B:334 , THR B:358BINDING SITE FOR RESIDUE ADP B 501
5AC5SOFTWAREASP A:160 , LYS A:342 , LYS A:374 , TRP B:395BINDING SITE FOR RESIDUE GOL A 502
6AC6SOFTWARETRP A:395 , ASP B:160 , LEU B:339 , LYS B:342 , LYS B:374BINDING SITE FOR RESIDUE GOL B 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3D2R)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3D2R)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

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

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3D2R)

(-) Exons   (11, 22)

Asymmetric/Biological Unit (11, 22)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000000051781aENSE00001133344chr7:95225803-95225476328PDK4_HUMAN1-44442A:21-44
B:20-44
24
25
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 (gaps)
63
63
1.4cENST000000051784cENSE00000706266chr7:95221909-9522182387PDK4_HUMAN177-206302A:177-206 (gaps)
B:177-206
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:291-327 (gaps)
37
37
1.8aENST000000051788aENSE00000706258chr7:95216435-95216322114PDK4_HUMAN328-365382A:328-365
B:328-365
38
38
1.9bENST000000051789bENSE00001267271chr7:95215093-952128112283PDK4_HUMAN366-411462A:366-397 (gaps)
B:366-397 (gaps)
32
32

(-) 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:377
                                    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 PREVEHFSRYSPSPLSMKQLLDFGSENACERTSFAFLRQELPVRLANILKEIDILPTQLVNTSSVQLVKSWYIQSLMDLVEFHEKSPDDQKALSDFVDTLIKVRNRHHNVVPTMAQGIIEYKDACTVDPVTNQNLQYFLDRFYMNRISTRMLMNQHILIFSDSQTGNPSHIGSIDPNCDVVAVVQDAFECSRMLCDQYYLSSPELKLTQVNGKFPDQPIHIVYVPSHLHHMLFELFKNAMRATVEHQENQPSLTPIEVIVVLGKEDLTIKISDRGGGVPLRIIDRLFSYTYSTAPTPVMDNSRNAPLAGFGYGLPISRLYAKYFQGDLNLYSLSGYGTDAIIYLKALSSESIEKLPVFNKSAFKHYQMSSEADDWCI 397
               SCOP domains d3d2ra1 A:21-180 automated  matches                                                                                                                             d3      d2ra2 A:181-397 automated matches                                                                                                                                                                                 SCOP domains
               CATH domains 3d2rA01 A:21-189  [code=1.2 0.140.20, no name defined]                                                                                                                   3d2rA02 A:190-374  [code=3.30.565.10, no name defined]                                                                                                                                   ------------      ----- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh......hhhhhhhh....-hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh--hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.------......eeeeehhhhhhhhhhhhhhhhhhhhh....eeeeeee........eeeehhhhhhhhhhhhhhhhhhhhhhhh........eeeeeee...eeeeeeee.....hhhhhhhhh.........--------.......hhhhhhhhhhhhh..eeeeeee...eeeeeeeee.........ee..hhhhhhhh------..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------G------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: A:21-44 ----------------------------------------------Exon 1.3  PDB: A:91-115  -------------------------------------------------------------Exon 1.4c UniProt: 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  PDB: A:366-397 (gaps) 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)
                 3d2r A  21 PREVEHFSRYSPSPLSMKQLLDFGSEN-CERTSFAFLRQELPVRLANILKEIDILPTQLVNTSSVQLVKSWYIQSLMDLVEFHEKSPDDQKALSDFVDTLIKVRNRHHNVVPTMAQGIIEYKDAC--DPVTNQNLQYFLDRFYMNRISTRMLMNQHILIFSD------SHIGSIDPNCDVVAVVQDAFECSRMLCDQYYLSSPELKLTQVNGKFPDQPIHIVYVPSHLHHMLFELFKNAMRATVEHQENQPSLTPIEVIVVLGKEDLTIKISDRGGGVPLRIIDRLFSYTYSTAPT--------APLAGFGYGLPISRLYAKYFQGDLNLYSLSGYGTDAIIYLKALSSESIEKLPVFNKSAFKHY------DDWCI 397
                                    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     |   -  |    
                                                     47 |                                                                                             145  |                               182    189                                                                                                                            316      325                                                          386    393    
                                                       49                                                                                                148                                                                                                                                                                                                                                                         

Chain B from PDB  Type:PROTEIN  Length:362
 aligned with PDK4_HUMAN | Q16654 from UniProtKB/Swiss-Prot  Length:411

    Alignment length:378
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389        
           PDK4_HUMAN    20 VPREVEHFSRYSPSPLSMKQLLDFGSENACERTSFAFLRQELPVRLANILKEIDILPTQLVNTSSVQLVKSWYIQSLMDLVEFHEKSPDDQKALSDFVDTLIKVRNRHHNVVPTMAQGIIEYKDACTVDPVTNQNLQYFLDRFYMNRISTRMLMNQHILIFSDSQTGNPSHIGSIDPNCDVVAVVQDAFECSRMLCDQYYLSSPELKLTQVNGKFPDQPIHIVYVPSHLHHMLFELFKNAMRATVEHQENQPSLTPIEVIVVLGKEDLTIKISDRGGGVPLRIIDRLFSYTYSTAPTPVMDNSRNAPLAGFGYGLPISRLYAKYFQGDLNLYSLSGYGTDAIIYLKALSSESIEKLPVFNKSAFKHYQMSSEADDWCI 397
               SCOP domains d3d2rb1 B:20-180 automated matches                                                                                                                               d3d2rb2 B:181-397 automated matches                                                                                                                                                                                       SCOP domains
               CATH domains 3d2rB01 B:20-189  [code=1.20.140.20, no name defined]                                                                                                                     3d2rB02 B:190-374  [code=3.30.565.10, no name defined]                                                                                                                                   ------------       ---- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhh......hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh-........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............eeeeehhhhhhhhhhhhhhhhhhhhh....eeeeeee........eeeehhhhhhhhhhhhhhhhhhhhhhhh........eeeeeee...eeeeeeee.....hhhhhhhhhh.........--------......hhhhhhhhhhhhh..eeeeeee...eeeeeeeee.............hhhhhhhh-------.... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------G------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: B:20-44  ----------------------------------------------Exon 1.3  PDB: B:91-115  -------------------------------------------------------------Exon 1.4c  PDB: B:177-206     -------------------------Exon 1.6b  PDB: B:232-257 Exon 1.7a  PDB: B:258-290        Exon 1.7d  PDB: B:291-327 (gaps)     Exon 1.8a  PDB: B:328-365             Exon 1.9b  PDB: B:366-397 (gaps) Transcript 1 (1)
           Transcript 1 (2) ------------------------Exon 1.2a  PDB: B:44-91 UniProt: 44-91          -----------------------Exon 1.4a  PDB: B:115-177 (gaps) UniProt: 115-177              ----------------------------Exon 1.5  PDB: B:206-232   --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 3d2r B  20 VPREVEHFSRYSPSPLSMKQLLDFGSENACERTSFAFLRQELPVRLANILKEIDILPTQLVNTSSVQLVKSWYIQSLMDLVEFHEKSPDDQKALSDFVDTLIKVRNRHHNVVPTMAQGIIEYK-ACTVDPVTNQNLQYFLDRFYMNRISTRMLMNQHILIFSDSQTGNPSHIGSIDPNCDVVAVVQDAFECSRMLCDQYYLSSPELKLTQVNGKFPDQPIHIVYVPSHLHHMLFELFKNAMRATVEHQENQPSLTPIEVIVVLGKEDLTIKISDRGGGVPLRIIDRLFSYTYSTAPTP--------PLAGFGYGLPISRLYAKYFQGDLNLYSLSGYGTDAIIYLKALSSESIEKLPVFNKSAFKHY-------DWCI 397
                                    29        39        49        59        69        79        89        99       109       119       129       139  | |  149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       | -      |329       339       349       359       369       379      |  -    |   
                                                                                                                                                    142 |                                                                                                                                                                          317      326                                                         386     394   
                                                                                                                                                      144                                                                                                                                                                                                                                                             

   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  (0, 0)

(no "Pfam Domain" information available for 3D2R)

(-) 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 2zdy 2zkj

(-) Related Entries Specified in the PDB File

2zkj CRYSTALLIZED IN PHOSPHATE BUFFER