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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN DOT1L IN COMPLEX WITH INHIBITOR EPZ004777
 
Authors :  A. K. Wernimont, W. Tempel, W. Yu, A. Scopton, Y. Li, K. T. Nguyen, A. Fede J. Marineau, J. Qi, M. Vedadi, J. E. Bradner, M. Schapira, C. H. Arrowsm A. M. Edwards, C. Bountra, P. J. Brown, Structural Genomics Consort
Date :  19 Apr 12  (Deposition) - 16 May 12  (Release) - 16 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Histone, Methyltransferase, Epigenetics, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. K. Wernimont, W. Tempel, W. Yu, A. Scopton, Y. Li, K. T. Nguyen, A. Federation, J. Marineau, J. Qi, M. Vedadi, J. E. Bradner, M. Schapira, C. H. Arrowsmith, A. M. Edwards, C. Bountra, P. J. Brown
Crystal Structure Of Human Dot1L In Complex With Inhibitor Epz004777
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-79 SPECIFIC
    Chains: A
    EC Number: 2.1.1.43
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28-MHL
    Expression System Strain: BL21 V2R PRARE2
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: DOT1L, KIAA1814, KMT4
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DOT1-LIKE PROTEIN, HISTONE H3-K79 METHYLTRANSFERASE, H3-K79- HMTASE, LYSINE N-METHYLTRANSFERASE 4

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 14)

Asymmetric/Biological Unit (4, 14)
No.NameCountTypeFull Name
10QK1Ligand/Ion7-{5-[(3-{[(4-TERT-BUTYLPHENYL)CARBAMOYL]AMINO}PROPYL)(PROPAN-2-YL)AMINO]-5-DEOXY-BETA-D-RIBOFURANOSYL}-7H-PYRROLO[2,3-D]PYRIMIDIN-4-AMINE
2EDO2Ligand/Ion1,2-ETHANEDIOL
3SO45Ligand/IonSULFATE ION
4UNX6Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET A:147 , ASP A:161 , GLY A:163 , SER A:164 , VAL A:169 , GLU A:186 , LYS A:187 , GLY A:221 , ASP A:222 , PHE A:223 , ASN A:241 , PHE A:245 , SER A:268 , TYR A:312BINDING SITE FOR RESIDUE 0QK A 401
2AC2SOFTWAREASN A:99 , ARG A:101BINDING SITE FOR RESIDUE SO4 A 402
3AC3SOFTWARETHR A:104BINDING SITE FOR RESIDUE SO4 A 403
4AC4SOFTWARESER A:67 , PHE A:68 , GLU A:69BINDING SITE FOR RESIDUE SO4 A 404
5AC5SOFTWAREHIS A:117 , GLU A:201 , LYS A:204 , LYS A:300BINDING SITE FOR RESIDUE SO4 A 405
6AC6SOFTWAREARG A:203 , LYS A:207 , HIS A:213BINDING SITE FOR RESIDUE SO4 A 406
7AC7SOFTWAREVAL A:160 , TYR A:183 , THR A:235BINDING SITE FOR RESIDUE EDO A 407
8AC8SOFTWAREARG A:229 , ARG A:256BINDING SITE FOR RESIDUE EDO A 408

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4ER3)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Trp A:22 -Pro A:23

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4ER3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4ER3)

(-) Exons   (0, 0)

(no "Exon" information available for 4ER3)

(-) 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:311
                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains d4er3a_ A: automated matches                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee........eeee....eee..eehhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhh......eeeee....hhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhhhhhhh.....eeeee....hhhhhhhhhh..eeee.....hhhhhhhhhhhhhh.....eeee.................hhhh.eeeeee........eeeeee.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4er3 A   4 KLELRLKSPVGAEPAVYPWPLPVYDKHHDAAHEIIETIRWVCEEIPDLKLAMENYVLIDYDTKSFESMQRLCDKYNRAIDSIHQLWKGTTQPMKLNTRPSTGLLRHILQQVYNHSVTDPEKLNNETSFDLVAQMIDEIKMTDDDLFVDLGSGVGQVVLQVAAATNCKHHYGVEKADIPAKYAETMDREFRKWMKWYGKKHAEYTLERGDFLSEEWRERIANTSVIFVNNFAFGPEVDHQLKERFANMKEGGRIVSSKPFAPLNFRINSRNLSDIGTIMRVVELSPLKGSVSYYLHTIDRTILENYFSSLKN 331
                                    13        23        33        43        53        63        73        83        93       103       113       123   ||  143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       310       320       330 
                                                                                                                                                     127|                                                                                                                                                                 302|                     
                                                                                                                                                      138                                                                                                                                                                  310
   Legend:   → Mismatch (orange background)
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  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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4ER3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4ER3)

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        DOT1L_HUMAN | Q8TEK3: 1nw3 2mv7 3qow 3qox 3sr4 3sx0 3uwp 4ek9 4ekg 4eki 4eqz 4er0 4er5 4er6 4er7 4hra 4wvl 5drt 5dry 5dsx 5dt2 5dtm 5dtq 5dtr 5juw 5mvs 5mw3 5mw4

(-) Related Entries Specified in the PDB File

4eqz 4er0 4er5 4er6 4er7