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(-) Description

Title :  STRUCTURAL DISSECTION OF HUMAN MITOGEN-ACTIVATED KINASE ERK1
 
Authors :  T. Kinoshita, T. Tada, S. Nakae, I. Yoshida
Date :  01 Jun 08  (Deposition) - 07 Apr 09  (Release) - 07 Apr 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.39
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Serine/Threonine Kinase, Erk1, Acetylation, Atp-Binding, Cell Cycle, Host-Virus Interaction, Nucleotide-Binding, Phosphoprotein, Polymorphism, Serine/Threonine-Protein Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Kinoshita, I. Yoshida, S. Nakae, K. Okita, M. Gouda, M. Matsubara, K. Yokota, H. Ishiguro, T. Tada
Crystal Structure Of Human Mono-Phosphorylated Erk1 At Tyr204
Biochem. Biophys. Res. Commun. V. 377 1123 2008
PubMed-ID: 18983981  |  Reference-DOI: 10.1016/J.BBRC.2008.10.127
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MITOGEN-ACTIVATED PROTEIN KINASE 3
    ChainsA, B
    EC Number2.7.11.24
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX-6P
    Expression System StrainJM109
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneMAPK3, ERK1, PRKM3
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymEXTRACELLULAR SIGNAL-REGULATED KINASE 1, ERK-1, INSULIN-STIMULATED MAP2 KINASE, MAP KINASE 1, MAPK 1, P44- ERK1, ERT2, P44-MAPK, MICROTUBULE-ASSOCIATED PROTEIN 2 KINASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric Unit (4, 8)
No.NameCountTypeFull Name
15ID2Ligand/Ion(2R,3R,4S,5R)-2-(4-AMINO-5-IODO-7H-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-(HYDROXYMETHYL)TETRAHYDROFURAN-3,4-DIOL
2NA2Ligand/IonSODIUM ION
3PTR2Mod. Amino AcidO-PHOSPHOTYROSINE
4SO42Ligand/IonSULFATE ION
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
15ID1Ligand/Ion(2R,3R,4S,5R)-2-(4-AMINO-5-IODO-7H-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-(HYDROXYMETHYL)TETRAHYDROFURAN-3,4-DIOL
2NA-1Ligand/IonSODIUM ION
3PTR1Mod. Amino AcidO-PHOSPHOTYROSINE
4SO41Ligand/IonSULFATE ION
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
15ID1Ligand/Ion(2R,3R,4S,5R)-2-(4-AMINO-5-IODO-7H-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-(HYDROXYMETHYL)TETRAHYDROFURAN-3,4-DIOL
2NA-1Ligand/IonSODIUM ION
3PTR1Mod. Amino AcidO-PHOSPHOTYROSINE
4SO41Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:208 , ARG A:211 , TYR A:250BINDING SITE FOR RESIDUE SO4 A 380
2AC2SOFTWAREARG B:84 , ARG B:165BINDING SITE FOR RESIDUE SO4 B 380
3AC3SOFTWARELYS B:71 , CYS B:183 , ASP B:184BINDING SITE FOR RESIDUE NA B 381
4AC4SOFTWARECYS A:183 , ASP A:184BINDING SITE FOR RESIDUE NA A 381
5AC5SOFTWAREILE B:48 , ALA B:69 , GLN B:122 , ASP B:123 , MET B:125 , ASP B:128 , LYS B:131 , SER B:170 , LEU B:173 , ASP B:184BINDING SITE FOR RESIDUE 5ID B 382
6AC6SOFTWAREILE A:48 , GLU A:50 , ALA A:69 , GLN A:122 , ASP A:123 , MET A:125 , SER A:170 , LEU A:173 , ASP A:184BINDING SITE FOR RESIDUE 5ID A 382

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Gly A:39 -Pro A:40
2Ile A:244 -Phe A:245
3Lys A:248 -His A:249
4Leu A:269 -Asn A:270
5Asn A:270 -Cys A:271
6Ala A:349 -Met A:350
7Gly B:39 -Pro B:40
8Glu B:203 -Ptr B:204

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 2)

Asymmetric Unit (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_042253E323KMK03_HUMANPolymorphism55859133A/BE323K

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_042253E323KMK03_HUMANPolymorphism55859133AE323K

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_042253E323KMK03_HUMANPolymorphism55859133BE323K

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

(-) PROSITE Motifs  (3, 6)

Asymmetric Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.MK03_HUMAN48-72
 
  2A:48-72
B:48-72
2MAPKPS01351 MAP kinase signature.MK03_HUMAN76-178
 
  2A:76-178
B:76-178
3PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.MK03_HUMAN162-174
 
  2A:162-174
B:162-174
Biological Unit 1 (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.MK03_HUMAN48-72
 
  1A:48-72
-
2MAPKPS01351 MAP kinase signature.MK03_HUMAN76-178
 
  1A:76-178
-
3PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.MK03_HUMAN162-174
 
  1A:162-174
-
Biological Unit 2 (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.MK03_HUMAN48-72
 
  1-
B:48-72
2MAPKPS01351 MAP kinase signature.MK03_HUMAN76-178
 
  1-
B:76-178
3PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.MK03_HUMAN162-174
 
  1-
B:162-174

(-) Exons   (0, 0)

(no "Exon" information available for 2ZOQ)

(-) 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:352
 aligned with MK03_HUMAN | P27361 from UniProtKB/Swiss-Prot  Length:379

    Alignment length:352
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373  
           MK03_HUMAN    24 VPGEVEMVKGQPFDVGPRYTQLQYIGEGAYGMVSSAYDHVRKTRVAIKKISPFEHQTYCQRTLREIQILLRFRHENVIGIRDILRASTLEAMRDVYIVQDLMETDLYKLLKSQQLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLINTTCDLKICDFGLARIADPEHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINMKARNYLQSLPSKTKVAWAKLFPKSDSKALDLLDRMLTFNPNKRITVEEALAHPYLEQYYDPTDEPVAEEPFTFAMELDDLPKERLKELIFQETARFQPGV 375
               SCOP domains d2zoqa_ A: automated matches                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 2zoqA01 A:24-124,A:356-373 Phosphorylase Kinase; domain 1                                            2zoqA02 A:125-355 Transferase(Phosphotransferase) domain 1                                                                                                                                                                             2zoqA01           -- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................eeeeeeee.....eeeeeee....eeeeeeee....hhhhhhhhhhhhhhhhhh.........eee..........eeeeee...eehhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee........eee.....eee......ee.hhhhh..........hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhh...........hhhhhhhhhhh......hhhhhh...hhhhhhhhhhhh........hhhhhhhhhhhh...hhhhh...........hhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------K---------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------PROTEIN_KINASE_ATP       ---MAPK  PDB: A:76-178 UniProt: 76-178                                                                    ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------PROTEIN_KINAS--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zoq A  24 VPGEVEMVKGQPFDVGPRYTQLQYIGEGAYGMVSSAYDHVRKTRVAIKKISPFEHQTYCQRTLREIQILLRFRHENVIGIRDILRASTLEAMRDVYIVQDLMETDLYKLLKSQQLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLINTTCDLKICDFGLARIADPEHDHTGFLTEyVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINMKARNYLQSLPSKTKVAWAKLFPKSDSKALDLLDRMLTFNPNKRITVEEALAHPYLEQYYDPTDEPVAEEPFTFAMELDDLPKERLKELIFQETARFQPGV 375
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203|      213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373  
                                                                                                                                                                                                              204-PTR                                                                                                                                                                       

Chain B from PDB  Type:PROTEIN  Length:352
 aligned with MK03_HUMAN | P27361 from UniProtKB/Swiss-Prot  Length:379

    Alignment length:352
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373  
           MK03_HUMAN    24 VPGEVEMVKGQPFDVGPRYTQLQYIGEGAYGMVSSAYDHVRKTRVAIKKISPFEHQTYCQRTLREIQILLRFRHENVIGIRDILRASTLEAMRDVYIVQDLMETDLYKLLKSQQLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLINTTCDLKICDFGLARIADPEHDHTGFLTEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINMKARNYLQSLPSKTKVAWAKLFPKSDSKALDLLDRMLTFNPNKRITVEEALAHPYLEQYYDPTDEPVAEEPFTFAMELDDLPKERLKELIFQETARFQPGV 375
               SCOP domains d2zoqb_ B: automated matches                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 2zoqB01 B:24-124,B:356-373 Phosphorylase Kinase; domain 1                                            2zoqB02 B:125-355 Transferase(Phosphotransferase) domain 1                                                                                                                                                                             2zoqB01           -- CATH domains
           Pfam domains (1) ------------------Pkinase-2zoqB01 B:42-330                                                                                                                                                                                                                                                                         --------------------------------------------- Pfam domains (1)
           Pfam domains (2) ------------------Pkinase-2zoqB02 B:42-330                                                                                                                                                                                                                                                                         --------------------------------------------- Pfam domains (2)
         Sec.struct. author .....eee..eee.....eeeeeeeeee..eeeeeeee....eeeeeeee....hhhhhhhhhhhhhhhhh..........eee..........eeeeee...eehhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee.hhhhh...............hhhhhh......hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh..hhhhhh...hhhhhhhhh........hhhhhh...hhhhhhhhhhhh........hhhhhhhhhhhh........................hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------K---------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------PROTEIN_KINASE_ATP       ---MAPK  PDB: B:76-178 UniProt: 76-178                                                                    ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------PROTEIN_KINAS--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zoq B  24 VPGEVEMVKGQPFDVGPRYTQLQYIGEGAYGMVSSAYDHVRKTRVAIKKISPFEHQTYCQRTLREIQILLRFRHENVIGIRDILRASTLEAMRDVYIVQDLMETDLYKLLKSQQLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLINTTCDLKICDFGLARIADPEHDHTGFLTEyVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINMKARNYLQSLPSKTKVAWAKLFPKSDSKALDLLDRMLTFNPNKRITVEEALAHPYLEQYYDPTDEPVAEEPFTFAMELDDLPKERLKELIFQETARFQPGV 375
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203|      213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373  
                                                                                                                                                                                                              204-PTR                                                                                                                                                                       

   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  (1, 2)

Asymmetric Unit

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: PKinase (934)

(-) Gene Ontology  (92, 92)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (MK03_HUMAN | P27361)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004707    MAP kinase activity    Catalysis of the reaction: protein + ATP = protein phosphate + ADP. This reaction is the phosphorylation of proteins. Mitogen-activated protein kinase; a family of protein kinases that perform a crucial step in relaying signals from the plasma membrane to the nucleus. They are activated by a wide range of proliferation- or differentiation-inducing signals; activation is strong with agonists such as polypeptide growth factors and tumor-promoting phorbol esters, but weak (in most cell backgrounds) by stress stimuli.
    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:0019902    phosphatase binding    Interacting selectively and non-covalently with any phosphatase.
    GO:0001784    phosphotyrosine residue binding    Interacting selectively and non-covalently with a phosphorylated tyrosine residue within a protein.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    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:0004674    protein serine/threonine kinase activity    Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
    GO:0097110    scaffold protein binding    Interacting selectively and non-covalently with a scaffold protein. Scaffold proteins are crucial regulators of many key signaling pathways. Although not strictly defined in function, they are known to interact and/or bind with multiple members of a signaling pathway, tethering them into complexes.
    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:0030509    BMP signaling pathway    A series of molecular signals initiated by the binding of a member of the BMP (bone morphogenetic protein) family to a receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0060020    Bergmann glial cell differentiation    The process in which neuroepithelial cells of the neural tube give rise to Brgmann glial cells, specialized bipotential progenitors cells of the cerebellum. Differentiation includes the processes involved in commitment of a cell to a specific fate.
    GO:0006975    DNA damage induced protein phosphorylation    The widespread phosphorylation of various molecules, triggering many downstream processes, that occurs in response to the detection of DNA damage.
    GO:0070371    ERK1 and ERK2 cascade    An intracellular protein kinase cascade containing at least ERK1 or ERK2 (MAPKs), a MEK (a MAPKK) and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.
    GO:0038095    Fc-epsilon receptor signaling pathway    A series of molecular signals initiated by the binding of the Fc portion of immunoglobulin E (IgE) to an Fc-epsilon receptor on the surface of a signal-receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription. The Fc portion of an immunoglobulin is its C-terminal constant region.
    GO:0038096    Fc-gamma receptor signaling pathway involved in phagocytosis    An Fc-gamma receptor signaling pathway that contributes to the endocytic engulfment of external particulate material by phagocytes.
    GO:0060397    JAK-STAT cascade involved in growth hormone signaling pathway    The process in which STAT proteins (Signal Transducers and Activators of Transcription) are activated by members of the JAK (janus activated kinase) family of tyrosine kinases, following the binding of physiological ligands to the growth hormone receptor. Once activated, STATs dimerize and translocate to the nucleus and modulate the expression of target genes.
    GO:0000165    MAPK cascade    An intracellular protein kinase cascade containing at least a MAPK, a MAPKK and a MAP3K. The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.
    GO:0000189    MAPK import into nucleus    The directed movement of a MAP kinase to the nucleus upon activation.
    GO:0000187    activation of MAPK activity    The initiation of the activity of the inactive enzyme MAP kinase (MAPK).
    GO:0009887    animal organ morphogenesis    Morphogenesis of an animal organ. An organ is defined as a tissue or set of tissues that work together to perform a specific function or functions. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0019369    arachidonic acid metabolic process    The chemical reactions and pathways involving arachidonic acid, a straight chain fatty acid with 20 carbon atoms and four double bonds per molecule. Arachidonic acid is the all-Z-(5,8,11,14)-isomer.
    GO:0007411    axon guidance    The chemotaxis process that directs the migration of an axon growth cone to a specific target site in response to a combination of attractive and repulsive cues.
    GO:0061308    cardiac neural crest cell development involved in heart development    The process aimed at the progression of a cardiac neural crest cell over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell that contributes to the development of the heart.
    GO:0051216    cartilage development    The process whose specific outcome is the progression of a cartilage element over time, from its formation to the mature structure. Cartilage elements are skeletal elements that consist of connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate.
    GO:0072584    caveolin-mediated endocytosis    An endocytosis process that begins when material is taken up into plasma membrane caveolae, which then pinch off to form endocytic caveolar carriers.
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0006974    cellular response to DNA damage stimulus    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 stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0071260    cellular response to mechanical stimulus    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 mechanical stimulus.
    GO:0060324    face development    The biological process whose specific outcome is the progression of a face from an initial condition to its mature state. The face is the ventral division of the head.
    GO:0008543    fibroblast growth factor receptor signaling pathway    The series of molecular signals generated as a consequence of a fibroblast growth factor receptor binding to one of its physiological ligands.
    GO:0070498    interleukin-1-mediated signaling pathway    A series of molecular signals initiated by the binding of interleukin-1 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0035556    intracellular signal transduction    The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
    GO:0031663    lipopolysaccharide-mediated signaling pathway    A series of molecular signals initiated by the binding of a lipopolysaccharide (LPS) to a receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription. Lipopolysaccharides are major components of the outer membrane of Gram-negative bacteria, making them prime targets for recognition by the immune system.
    GO:0060425    lung morphogenesis    The process in which the anatomical structures of the lung are generated and organized.
    GO:2000657    negative regulation of apolipoprotein binding    Any process that stops, prevents or reduces the frequency, rate or extent of apolipoprotein binding.
    GO:0014032    neural crest cell development    The process aimed at the progression of a neural crest cell over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell.
    GO:0042473    outer ear morphogenesis    The process in which the anatomical structures of the outer ear are generated and organized. The outer ear is the part of the ear external to the tympanum (eardrum). It consists of a tube (the external auditory meatus) that directs sound waves on to the tympanum, and may also include the external pinna, which extends beyond the skull.
    GO:0018105    peptidyl-serine phosphorylation    The phosphorylation of peptidyl-serine to form peptidyl-O-phospho-L-serine.
    GO:0038083    peptidyl-tyrosine autophosphorylation    The phosphorylation by a protein of one or more of its own tyrosine amino acid residues, or a tyrosine residue on an identical protein.
    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:0030168    platelet activation    A series of progressive, overlapping events triggered by exposure of the platelets to subendothelial tissue. These events include shape change, adhesiveness, aggregation, and release reactions. When carried through to completion, these events lead to the formation of a stable hemostatic plug.
    GO:0070374    positive regulation of ERK1 and ERK2 cascade    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
    GO:0031281    positive regulation of cyclase activity    Any process that activates or increases the activity of a cyclase.
    GO:0035066    positive regulation of histone acetylation    Any process that activates or increases the frequency, rate or extent of the addition of an acetyl group to a histone protein.
    GO:0033129    positive regulation of histone phosphorylation    Any process that activates or increases the frequency, rate or extent of the addition of one or more phosphate groups to a histone protein.
    GO:0001934    positive regulation of protein phosphorylation    Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to amino acids within a protein.
    GO:0051973    positive regulation of telomerase activity    Any process that activates or increases the frequency, rate or extent of telomerase activity, the catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).
    GO:1904355    positive regulation of telomere capping    Any process that activates or increases the frequency, rate or extent of telomere capping.
    GO:0032212    positive regulation of telomere maintenance via telomerase    Any process that activates or increases the frequency, rate or extent of the addition of telomeric repeats by telomerase.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0045727    positive regulation of translation    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    GO:1904417    positive regulation of xenophagy    Any process that activates or increases the frequency, rate or extent of xenophagy.
    GO:0006461    protein complex assembly    The aggregation, arrangement and bonding together of a set of components to form a protein complex.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0090170    regulation of Golgi inheritance    Any process that modulates the rate, frequency or extent of Golgi inheritance. Golgi inheritance is the partitioning of Golgi apparatus between daughter cells at cell division.
    GO:1900034    regulation of cellular response to heat    Any process that modulates the frequency, rate or extent of cellular response to heat.
    GO:0051493    regulation of cytoskeleton organization    Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures.
    GO:2000641    regulation of early endosome to late endosome transport    Any process that modulates the frequency, rate or extent of early endosome to late endosome transport.
    GO:0014066    regulation of phosphatidylinositol 3-kinase signaling    Any process that modulates the frequency, rate or extent of signal transduction mediated by the phosphatidylinositol 3-kinase cascade.
    GO:0051090    regulation of sequence-specific DNA binding transcription factor activity    Any process that modulates the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
    GO:0032872    regulation of stress-activated MAPK cascade    Any process that modulates the frequency, rate or extent of signal transduction mediated by the stress-activated MAPK cascade.
    GO:0070849    response to epidermal growth factor    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 an epidermal growth factor stimulus.
    GO:0043330    response to exogenous dsRNA    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 an exogenous double-stranded RNA stimulus.
    GO:0032496    response to lipopolysaccharide    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    GO:0009636    response to toxic substance    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 toxic stimulus.
    GO:0019233    sensory perception of pain    The series of events required for an organism to receive a painful stimulus, convert it to a molecular signal, and recognize and characterize the signal. Pain is medically defined as the physical sensation of discomfort or distress caused by injury or illness, so can hence be described as a harmful stimulus which signals current (or impending) tissue damage. Pain may come from extremes of temperature, mechanical damage, electricity or from noxious chemical substances. This is a neurological process.
    GO:0048538    thymus development    The process whose specific outcome is the progression of the thymus over time, from its formation to the mature structure. The thymus is a symmetric bi-lobed organ involved primarily in the differentiation of immature to mature T cells, with unique vascular, nervous, epithelial, and lymphoid cell components.
    GO:0030878    thyroid gland development    The process whose specific outcome is the progression of the thyroid gland over time, from its formation to the mature structure. The thyroid gland is an endoderm-derived gland that produces thyroid hormone.
    GO:0060440    trachea formation    The process pertaining to the initial formation of a trachea from unspecified parts. The process begins with the specific processes that contribute to the appearance of the discrete structure and ends when the trachea is recognizable. The trachea is the portion of the airway that attaches to the bronchi as it branches.
    GO:0006361    transcription initiation from RNA polymerase I promoter    Any process involved in the assembly of the RNA polymerase I preinitiation complex (PIC) at an RNA polymerase I promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. Promoter clearance, or release, is the transition between the initiation and elongation phases of transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0005901    caveola    A membrane raft that forms small pit, depression, or invagination that communicates with the outside of a cell and extends inward, indenting the cytoplasm and the cell membrane. Examples include flask-shaped invaginations of the plasma membrane in adipocytes associated with caveolin proteins, and minute pits or incuppings of the cell membrane formed during pinocytosis. Caveolae may be pinched off to form free vesicles within the cytoplasm.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005769    early endosome    A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
    GO:0005770    late endosome    A prelysosomal endocytic organelle differentiated from early endosomes by lower lumenal pH and different protein composition. Late endosomes are more spherical than early endosomes and are mostly juxtanuclear, being concentrated near the microtubule organizing center.
    GO:0015630    microtubule cytoskeleton    The part of the cytoskeleton (the internal framework of a cell) composed of microtubules and associated proteins.
    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.
    GO:0005635    nuclear envelope    The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space).
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
    GO:0031143    pseudopodium    A temporary protrusion or retractile process of a cell, associated with flowing movements of the protoplasm, and serving for locomotion and feeding.

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