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(-) Description

Title :  PHOSPHORYLATED MAP KINASE P38-GAMMA
 
Authors :  S. Bellon, M. J. Fitzgibbon, T. Fox, H. M. Hsiao, K. P. Wilson
Date :  17 May 99  (Deposition) - 17 May 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  P38-Gamma, Gamma, Phosphorylation, Map Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Bellon, M. J. Fitzgibbon, T. Fox, H. M. Hsiao, K. P. Wilson
The Structure Of Phosphorylated P38Gamma Is Monomeric And Reveals A Conserved Activation-Loop Conformation.
Structure Fold. Des. V. 7 1057 1999
PubMed-ID: 10508788  |  Reference-DOI: 10.1016/S0969-2126(99)80173-7
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHOSPHORYLATED MAP KINASE P38-GAMMA
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymSTRESS-ACTIVATED PROTEIN KINASE-3, ERK6, ERK5

 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, 10)

Asymmetric Unit (4, 10)
No.NameCountTypeFull Name
1ANP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2MG4Ligand/IonMAGNESIUM ION
3PTR2Mod. Amino AcidO-PHOSPHOTYROSINE
4TPO2Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1ANP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION
3PTR1Mod. Amino AcidO-PHOSPHOTYROSINE
4TPO1Mod. Amino AcidPHOSPHOTHREONINE
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
1ANP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2MG-1Ligand/IonMAGNESIUM ION
3PTR1Mod. Amino AcidO-PHOSPHOTYROSINE
4TPO1Mod. Amino AcidPHOSPHOTHREONINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:158 , ASP A:171 , ANP A:400 , HOH A:2039BINDING SITE FOR RESIDUE MG A 401
2AC2SOFTWAREASP A:171 , ANP A:400 , HOH A:2152 , HOH A:2153BINDING SITE FOR RESIDUE MG A 402
3AC3SOFTWAREASN B:1158 , ASP B:1171 , ANP B:1400BINDING SITE FOR RESIDUE MG B 1401
4AC4SOFTWAREASP B:1171 , ANP B:1400 , HOH B:2118BINDING SITE FOR RESIDUE MG B 1402
5AC5SOFTWAREVAL A:41 , ALA A:54 , LYS A:56 , ILE A:87 , MET A:109 , PRO A:110 , MET A:112 , ASP A:115 , LYS A:155 , GLY A:157 , ASN A:158 , LEU A:170 , ASP A:171 , MG A:401 , MG A:402 , HOH A:2039 , HOH A:2111 , HOH A:2152BINDING SITE FOR RESIDUE ANP A 400
6AC6SOFTWAREVAL B:1041 , ALA B:1054 , LYS B:1056 , ILE B:1087 , MET B:1109 , PRO B:1110 , MET B:1112 , ASP B:1115 , LYS B:1155 , GLY B:1157 , ASN B:1158 , LEU B:1170 , ASP B:1171 , MG B:1401 , MG B:1402 , HOH B:2002 , HOH B:2037 , HOH B:2053 , HOH B:2185 , HOH B:2186BINDING SITE FOR RESIDUE ANP B 1400

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1CM8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1CM8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 6)

Asymmetric Unit (3, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_042265T103MMK12_HUMANPolymorphism34422484A
B
T103
1103
M
2UniProtVAR_042266D230NMK12_HUMANPolymorphism35396905A
B
D230
1230
N
3UniProtVAR_012002T244MMK12_HUMANPolymorphism2066776A
B
T244
1244
M

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_042265T103MMK12_HUMANPolymorphism34422484A
A
T103
1103
M
2UniProtVAR_042266D230NMK12_HUMANPolymorphism35396905A
A
D230
1230
N
3UniProtVAR_012002T244MMK12_HUMANPolymorphism2066776A
A
T244
1244
M

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_042265T103MMK12_HUMANPolymorphism34422484A
B
T103
1103
M
2UniProtVAR_042266D230NMK12_HUMANPolymorphism35396905A
B
D230
1230
N
3UniProtVAR_012002T244MMK12_HUMANPolymorphism2066776A
B
T244
1244
M

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

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.MK12_HUMAN33-57
 
  2A:33-57
B:1033-1057
2MAPKPS01351 MAP kinase signature.MK12_HUMAN62-165
 
  2A:62-165
B:1062-1165
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.MK12_HUMAN33-57
 
  1A:33-57
-
2MAPKPS01351 MAP kinase signature.MK12_HUMAN62-165
 
  1A:62-165
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.MK12_HUMAN33-57
 
  1-
B:1033-1057
2MAPKPS01351 MAP kinase signature.MK12_HUMAN62-165
 
  1-
B:1062-1165

(-) Exons   (12, 24)

Asymmetric Unit (12, 24)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002156591aENSE00001825407chr22:50700254-50699814441MK12_HUMAN1-42422A:8-42 (gaps)
B:1008-1042 (gaps)
35
35
1.1hENST000002156591hENSE00001615312chr22:50699725-50699596130MK12_HUMAN42-85442A:42-85
B:1042-1085
44
44
1.2ENST000002156592ENSE00001709414chr22:50696730-5069667259MK12_HUMAN86-105202A:86-105
B:1086-1105
20
20
1.5aENST000002156595aENSE00001733788chr22:50695622-50695511112MK12_HUMAN105-142382A:105-142
B:1105-1142
38
38
1.5cENST000002156595cENSE00001673343chr22:50695393-5069536430MK12_HUMAN143-152102A:143-152
B:1143-1152
10
10
1.5eENST000002156595eENSE00001648986chr22:50695075-5069502848MK12_HUMAN153-168162A:153-168
B:1153-1168
16
16
1.6aENST000002156596aENSE00001733683chr22:50694628-50694514115MK12_HUMAN169-207392A:169-207
B:1169-1207
39
39
1.6dENST000002156596dENSE00001806010chr22:50694310-5069423972MK12_HUMAN207-231252A:207-231
B:1207-1231
25
25
1.6eENST000002156596eENSE00001648285chr22:50694123-5069404480MK12_HUMAN231-257272A:231-257
B:1231-1257
27
27
1.7ENST000002156597ENSE00000657617chr22:50693960-5069388279MK12_HUMAN258-284272A:258-284
B:1258-1284
27
27
1.8aENST000002156598aENSE00001320185chr22:50693799-50693626174MK12_HUMAN284-342592A:284-342 (gaps)
B:1284-1342 (gaps)
59
59
1.9cENST000002156599cENSE00001522805chr22:50691909-50691332578MK12_HUMAN342-367262A:342-353
B:1342-1353
12
12

(-) 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:329
 aligned with MK12_HUMAN | P53778 from UniProtKB/Swiss-Prot  Length:367

    Alignment length:346
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347      
          MK12_HUMAN      8 RSGFYRQEVTKTAWEVRAVYRDLQPVGSGAYGAVCSAVDGRTGAKVAIKKLYRPFQSELFAKRAYRELRLLKHMRHENVIGLLDVFTPDETLDDFTDFYLVMPFMGTDLGKLMKHEKLGEDRIQFLVYQMLKGLRYIHAAGIIHRDLKPGNLAVNEDCELKILDFGLARQADSEMTGYVVTRWYRAPEVILNWMRYTQTVDIWSVGCIMAEMITGKTLFKGSDHLDQLKEIMKVTGTPPAEFVQRLQSDEAKNYMKGLPELEKKDFASILTNASPLAVNLLEKMLVLDAEQRVTAGEALAHPYFESLHDTEDEPQVQKYDDSFDDVDRTLDEWKRVTYKEVLSFKP  353
               SCOP domains d1cm8a_ A: MAP kinase p38-      gamma                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------1cm8A01 A:      24-113 Phosphorylase Kinase; domain 1                                     1cm8A02 A:114-328 Transferase(Phosphotransferase) domain 1                                                                                                                                                             -     ------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........................------eeeeee......eeeeee.......hhhhhhhhhhhhhhhh........eeeee............eeeee.....hhhhhhh....hhhhhhhhhhhhhhhhhhhh.........hhheee.....eee...................hhh..hhhhh......hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhh....hhhhhh...hhhhhhhhh........hhh......hhhhhhhhhh..........hhhhhh.hhh....------........-----..hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------PROTEIN_KINASE_ATP       ----MAPK  PDB: A:62-165 UniProt: 62-165                                                                     -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: A:8-42 (gaps)      -------------------------------------------Exon 1.2            -------------------------------------Exon 1.5c Exon 1.5e       Exon 1.6a  PDB: A:169-207              -----------------------Exon 1.6e  PDB: A:231-257  Exon 1.7  PDB: A:258-284   ---------------------------------------------------------Exon 1.9c    Transcript 1 (1)
           Transcript 1 (2) ----------------------------------Exon 1.1h  PDB: A:42-85 UniProt: 42-85      -------------------Exon 1.5a  PDB: A:105-142             ----------------------------------------------------------------Exon 1.6d  PDB: A:207-231----------------------------------------------------Exon 1.8a  PDB: A:284-342 (gaps) UniProt: 284-342          ----------- Transcript 1 (2)
                1cm8 A    8 RSGFYRQEVTKTAWEVRAVYRDLQPV------AVCSAVDGRTGAKVAIKKLYRPFQSELFAKRAYRELRLLKHMRHENVIGLLDVFTPDETLDDFTDFYLVMPFMGTDLGKLMKHEKLGEDRIQFLVYQMLKGLRYIHAAGIIHRDLKPGNLAVNEDCELKILDFGLARQADSEMtGyVVTRWYRAPEVILNWMRYTQTVDIWSVGCIMAEMITGKTLFKGSDHLDQLKEIMKVTGTPPAEFVQRLQSDEAKNYMKGLPELEKKDFASILTNASPLAVNLLEKMLVLDAEQRVTAGEALAHPYFESLH------QVQKYDDS-----RTLDEWKRVTYKEVLSFKP  353
                                    17        27     |   -  |     47        57        67        77        87        97       107       117       127       137       147       157       167       177     | 187       197       207       217       227       237       247       257       267       277       287       297       307       | -    |  327 |     337       347      
                                                    33     40                                                                                                                                            183-TPO                                                                                                                             315    322    329   335                  
                                                                                                                                                                                                           185-PTR                                                                                                                                                                    

Chain B from PDB  Type:PROTEIN  Length:329
 aligned with MK12_HUMAN | P53778 from UniProtKB/Swiss-Prot  Length:367

    Alignment length:346
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347      
          MK12_HUMAN      8 RSGFYRQEVTKTAWEVRAVYRDLQPVGSGAYGAVCSAVDGRTGAKVAIKKLYRPFQSELFAKRAYRELRLLKHMRHENVIGLLDVFTPDETLDDFTDFYLVMPFMGTDLGKLMKHEKLGEDRIQFLVYQMLKGLRYIHAAGIIHRDLKPGNLAVNEDCELKILDFGLARQADSEMTGYVVTRWYRAPEVILNWMRYTQTVDIWSVGCIMAEMITGKTLFKGSDHLDQLKEIMKVTGTPPAEFVQRLQSDEAKNYMKGLPELEKKDFASILTNASPLAVNLLEKMLVLDAEQRVTAGEALAHPYFESLHDTEDEPQVQKYDDSFDDVDRTLDEWKRVTYKEVLSFKP  353
               SCOP domains d1cm8b_ B: MAP kinase p38-      gamma                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------1cm8B01 B:      1024-1113 Phosphorylase Kinase; domain 1                                  1cm8B02 B:1114-1328 Transferase(Phosphotransferase) domain 1                                                                                                                                                           -     ------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........................------eeeeee......eeeeee.......hhhhhhhhhhhhhhhh........eeeee............eeeee.....hhhhhhh....hhhhhhhhhhhhhhhhhhhh.........hhheee.....eee...................hhh..hhhhh......hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhh....hhhhhh...hhhhhhhhh........hhh......hhhhhhhhhh..........hhhhhh.hhh....------........-----..hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------M------------------------------------------------------------------------------------------------------------------------------N-------------M------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------PROTEIN_KINASE_ATP       ----MAPK  PDB: B:1062-1165 UniProt: 62-165                                                                  -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: B:1008-1042 (gaps) -------------------------------------------Exon 1.2            -------------------------------------Exon 1.5c Exon 1.5e       Exon 1.6a  PDB: B:1169-1207            -----------------------Exon 1.6e  PDB: B:1231-1257Exon 1.7  PDB: B:1258-1284 ---------------------------------------------------------Exon 1.9c    Transcript 1 (1)
           Transcript 1 (2) ----------------------------------Exon 1.1h  PDB: B:1042-1085 UniProt: 42-85  -------------------Exon 1.5a  PDB: B:1105-1142           ----------------------------------------------------------------Exon 1.6d                ----------------------------------------------------Exon 1.8a  PDB: B:1284-1342 (gaps) UniProt: 284-342        ----------- Transcript 1 (2)
                1cm8 B 1008 RSGFYRQEVTKTAWEVRAVYRDLQPV------AVCSAVDGRTGAKVAIKKLYRPFQSELFAKRAYRELRLLKHMRHENVIGLLDVFTPDETLDDFTDFYLVMPFMGTDLGKLMKHEKLGEDRIQFLVYQMLKGLRYIHAAGIIHRDLKPGNLAVNEDCELKILDFGLARQADSEMtGyVVTRWYRAPEVILNWMRYTQTVDIWSVGCIMAEMITGKTLFKGSDHLDQLKEIMKVTGTPPAEFVQRLQSDEAKNYMKGLPELEKKDFASILTNASPLAVNLLEKMLVLDAEQRVTAGEALAHPYFESLH------QVQKYDDS-----RTLDEWKRVTYKEVLSFKP 1353
                                  1017      1027     |   -  |   1047      1057      1067      1077      1087      1097      1107      1117      1127      1137      1147      1157      1167      1177     |1187      1197      1207      1217      1227      1237      1247      1257      1267      1277      1287      1297      1307       | -    | 1327 |    1337      1347      
                                                  1033   1040                                                                                                                                           1183-TPO                                                                                                                            1315   1322   1329  1335                  
                                                                                                                                                                                                          1185-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  (0, 0)

(no "Pfam Domain" information available for 1CM8)

(-) Gene Ontology  (31, 31)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (MK12_HUMAN | P53778)
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:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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: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: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: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: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: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:0007050    cell cycle arrest    A regulatory process that halts progression through the cell cycle during one of the normal phases (G1, S, G2, M).
    GO:0007517    muscle organ development    The process whose specific outcome is the progression of the muscle over time, from its formation to the mature structure. The muscle is an organ consisting of a tissue made up of various elongated cells that are specialized to contract and thus to produce movement and mechanical work.
    GO:0045445    myoblast differentiation    The process in which a relatively unspecialized cell acquires specialized features of a myoblast. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into striated muscle fibers.
    GO:0045786    negative regulation of cell cycle    Any process that stops, prevents or reduces the rate or extent of progression through the cell cycle.
    GO:0018105    peptidyl-serine phosphorylation    The phosphorylation of peptidyl-serine to form peptidyl-O-phospho-L-serine.
    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:0051149    positive regulation of muscle cell differentiation    Any process that activates or increases the frequency, rate or extent of muscle cell differentiation.
    GO:0010952    positive regulation of peptidase activity    Any process that increases the frequency, rate or extent of peptidase activity, the hydrolysis of peptide bonds within proteins.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0048010    vascular endothelial growth factor receptor signaling pathway    Any series of molecular signals initiated by the binding of an extracellular ligand to a vascular endothelial growth factor receptor (VEGFR) located on the surface of the receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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: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: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.

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