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(-) Description

Title :  THE CRYSTAL STRUCTURE OF THE HUMAN MYOSIN LIGHT CHAIN KINASE LOC340156.
 
Authors :  J. R. C. Muniz, P. Mahajan, P. Rellos, O. Fedorov, B. Shrestha, J. Wang, J. M. Elkins, N. Daga, R. Cocking, A. Chaikuad, T. Krojer, E. Ugochukwu F. Von Delft, C. H. Arrowsmith, A. M. Edwards, J. Weigelt, C. Bountra, O. Gileadi, S. Knapp
Date :  29 Jan 10  (Deposition) - 09 Feb 10  (Release) - 05 Dec 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.67
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Lung, Kinase, Myosin, Breast Cancer, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. R. C. Muniz, P. Mahajan, P. Rellos, O. Fedorov, B. Shrestha, J. Wang, J. M. Elkins, N. Daga, R. Cocking, A. Chaikuad, T. Krojer, E. Ugochukwu W. Yue, F. Von Delft, C. H. Arrowsmith, A. M. Edwards, J. Weigelt, C. Bountra, O. Gileadi, S. Knapp
The Crystal Structure Of The Human Myosin Light Chain Kinase Loc340156
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - MYOSIN LIGHT CHAIN KINASE FAMILY MEMBER 4
    ChainsA, B
    EC Number2.7.11.1
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System Cell LineSF9
    Expression System Taxid7108
    Expression System VectorPFB-LIC-BSE
    Expression System Vector TypeBACULOVIRUS
    FragmentLIGHT CHAIN, RESIDUES 40-388
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymSERINE/THREONINE-PROTEIN KINASE SGK085, SUGEN KINASE 85

 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, 7)

Asymmetric Unit (4, 7)
No.NameCountTypeFull Name
116X2Ligand/Ion4-(2-AMINO-4-METHYL-1,3-THIAZOL-5-YL)-N-(3-DIOXAZIRIDIN-3-YLPHENYL)PYRIMIDIN-2-AMINE
21PE1Ligand/IonPENTAETHYLENE GLYCOL
3EDO3Ligand/Ion1,2-ETHANEDIOL
4SO41Ligand/IonSULFATE ION
Biological Unit 1 (4, 5)
No.NameCountTypeFull Name
116X1Ligand/Ion4-(2-AMINO-4-METHYL-1,3-THIAZOL-5-YL)-N-(3-DIOXAZIRIDIN-3-YLPHENYL)PYRIMIDIN-2-AMINE
21PE1Ligand/IonPENTAETHYLENE GLYCOL
3EDO2Ligand/Ion1,2-ETHANEDIOL
4SO41Ligand/IonSULFATE ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
116X1Ligand/Ion4-(2-AMINO-4-METHYL-1,3-THIAZOL-5-YL)-N-(3-DIOXAZIRIDIN-3-YLPHENYL)PYRIMIDIN-2-AMINE
21PE-1Ligand/IonPENTAETHYLENE GLYCOL
3EDO1Ligand/Ion1,2-ETHANEDIOL
4SO4-1Ligand/IonSULFATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU B:112 , GLY B:113 , VAL B:120 , GLU B:181 , VAL B:183 , GLY B:186 , LEU B:188 , LEU B:234 , ILE B:246BINDING SITE FOR RESIDUE 16X B1371
2AC2SOFTWARELEU A:112 , GLY A:113 , VAL A:120 , MET A:180 , GLU A:181 , TYR A:182 , VAL A:183 , GLY A:186 , ILE A:246BINDING SITE FOR RESIDUE 16X A1374
3AC3SOFTWARESER A:353 , LYS A:357 , HOH A:2118 , HOH A:2119 , HOH A:2120 , LYS B:255BINDING SITE FOR RESIDUE SO4 A1375
4AC4SOFTWAREGLN A:157 , ARG A:253 , HIS B:219 , TYR B:222 , PHE B:282BINDING SITE FOR RESIDUE 1PE A1376
5AC5SOFTWARELEU A:226 , ASP A:227 , LEU A:228 , PHE A:269 , LEU A:270 , SER A:288BINDING SITE FOR RESIDUE EDO A1377
6AC6SOFTWAREARG B:252 , LYS B:261BINDING SITE FOR RESIDUE EDO B1372
7AC7SOFTWAREARG A:252 , LYS A:261BINDING SITE FOR RESIDUE EDO A1378

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2X4F)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2X4F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (5, 9)

Asymmetric Unit (5, 9)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_040867T126MMYLK4_HUMANPolymorphism34953021A/BT126M
2UniProtVAR_040868H217LMYLK4_HUMANUnclassified  ---A/BH217L
3UniProtVAR_040869C318YMYLK4_HUMANPolymorphism35609073A/BC318Y
4CancerSNPVAR_MYLK4_HUMAN_CCDS10723_1_01 *L366RMYLK4_HUMANDisease (Colorectal cancer)  ---A/BG366R
5UniProtVAR_040870Q373RMYLK4_HUMANPolymorphism35211631AQ373R
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (5, 5)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_040867T126MMYLK4_HUMANPolymorphism34953021AT126M
2UniProtVAR_040868H217LMYLK4_HUMANUnclassified  ---AH217L
3UniProtVAR_040869C318YMYLK4_HUMANPolymorphism35609073AC318Y
4CancerSNPVAR_MYLK4_HUMAN_CCDS10723_1_01 *L366RMYLK4_HUMANDisease (Colorectal cancer)  ---AG366R
5UniProtVAR_040870Q373RMYLK4_HUMANPolymorphism35211631AQ373R
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_040867T126MMYLK4_HUMANPolymorphism34953021BT126M
2UniProtVAR_040868H217LMYLK4_HUMANUnclassified  ---BH217L
3UniProtVAR_040869C318YMYLK4_HUMANPolymorphism35609073BC318Y
4CancerSNPVAR_MYLK4_HUMAN_CCDS10723_1_01 *L366RMYLK4_HUMANDisease (Colorectal cancer)  ---BG366R
   * ID not provided by source

  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.MYLK4_HUMAN112-135
 
  2A:112-135
B:112-135
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.MYLK4_HUMAN223-235
 
  2A:223-235
B:223-235
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.MYLK4_HUMAN112-135
 
  1A:112-135
-
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.MYLK4_HUMAN223-235
 
  1A:223-235
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.MYLK4_HUMAN112-135
 
  1-
B:112-135
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.MYLK4_HUMAN223-235
 
  1-
B:223-235

(-) Exons   (0, 0)

(no "Exon" information available for 2X4F)

(-) 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:289
 aligned with MYLK4_HUMAN | Q86YV6 from UniProtKB/Swiss-Prot  Length:388

    Alignment length:294
                                    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    
          MYLK4_HUMAN    80 DIPAPPAPFDHRIVTAKQGAVNSFYTVSKTEILGGGRFGQVHKCEETATGLKLAAKIIKTRGMKDKEEVKNEISVMNQLDHANLIQLYDAFESKNDIVLVMEYVDGGELFDRIIDESYNLTELDTILFMKQICEGIRHMHQMYILHLDLKPENILCVNRDAKQIKIIDFGLARRYKPREKLKVNFGTPEFLAPEVVNYDFVSFPTDMWSVGVIAYMLLSGLSPFLGDNDAETLNNILACRWDLEDEEFQDISEEAKEFISKLLIKEKSWRISASEALKHPWLSDHKLHSRLNAQ 373
               SCOP domains d2x4fa_ A: automated matches                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ................ee.hhhh.eeeeeeee..-----.eeeeee.....eeeeeeee..hhhhhhhhhhhhhhhh.........eeeeee...eeeeeee.....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eeeee....eeee......ee.................hhhhhh....hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh.....hhhhh..hhhhhhhhhh....hhhhh.hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------M------------------------------------------------------------------------------------------L----------------------------------------------------------------------------------------------------Y------------------------------------------------------R SAPs(SNPs)
                    PROSITE --------------------------------PROTEIN_KINASE_ATP      ---------------------------------------------------------------------------------------PROTEIN_KINAS------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2x4f A  80 DIPAPPAPFDHRIVTAKQGAVNSFYTVSKTEILG-----QVHKCEETATGLKLAAKIIKTRGMKDKEEVKNEISVMNQLDHANLIQLYDAFESKNDIVLVMEYVDGGELFDRIIDESYNLTELDTILFMKQICEGIRHMHQMYILHLDLKPENILCVNRDAKQIKIIDFGLARRYKPREKLKVNFGTPEFLAPEVVNYDFVSFPTDMWSVGVIAYMLLSGLSPFLGDNDAETLNNILACRWDLEDEEFQDISEEAKEFISKLLIKEKSWRISASEALKHPWLSDHKLHSRLSAQ 373
                                    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    
                                                           113   119                                                                                                                                                                                                                                                              

Chain B from PDB  Type:PROTEIN  Length:288
 aligned with MYLK4_HUMAN | Q86YV6 from UniProtKB/Swiss-Prot  Length:388

    Alignment length:290
                                    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
          MYLK4_HUMAN    81 IPAPPAPFDHRIVTAKQGAVNSFYTVSKTEILGGGRFGQVHKCEETATGLKLAAKIIKTRGMKDKEEVKNEISVMNQLDHANLIQLYDAFESKNDIVLVMEYVDGGELFDRIIDESYNLTELDTILFMKQICEGIRHMHQMYILHLDLKPENILCVNRDAKQIKIIDFGLARRYKPREKLKVNFGTPEFLAPEVVNYDFVSFPTDMWSVGVIAYMLLSGLSPFLGDNDAETLNNILACRWDLEDEEFQDISEEAKEFISKLLIKEKSWRISASEALKHPWLSDHKLHSRL 370
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------------Pkinase-2x  4fB01 B:106-361                                                                                                                                                                                                                                     --------- Pfam domains (1)
           Pfam domains (2) -------------------------Pkinase-2x  4fB02 B:106-361                                                                                                                                                                                                                                     --------- Pfam domains (2)
         Sec.struct. author ...............ee.hhhh.eeeeeeeeee..--..eeeeee.....eeeeeeee..hhhhhhhhhhhhhhhh.........eeeeee...eeeeeee.....eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eeeee....eeee......ee.................hhhhhh....hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh......hhhhh..hhhhhhhhhh....hhhhh.hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------M------------------------------------------------------------------------------------------L----------------------------------------------------------------------------------------------------Y---------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------PROTEIN_KINASE_ATP      ---------------------------------------------------------------------------------------PROTEIN_KINAS--------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2x4f B  81 IPAPPAPFDHRIVTAKQGAVNSFYTVSKTEILGGG--GQVHKCEETATGLKLAAKIIKTRGMKDKEEVKNEISVMNQLDHANLIQLYDAFESKNDIVLVMEYVDGGELFDRIIDESYNLTELDTILFMKQICEGIRHMHQMYILHLDLKPENILCVNRDAKQIKIIDFGLARRYKPREKLKVNFGTPEFLAPEVVNYDFVSFPTDMWSVGVIAYMLLSGLSPFLGDNDAETLNNILACRWDLEDEEFQDISEEAKEFISKLLIKEKSWRISASEALKHPWLSDHKLHSRL 370
                                    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
                                                            115  |                                                                                                                                                                                                                                                            
                                                               118                                                                                                                                                                                                                                                            

   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, 1)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2X4F)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: PKinase (934)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (MYLK4_HUMAN | Q86YV6)
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: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: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:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
cellular component
    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.

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