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(-) Description

Title :  STRUCTURE-GUIDED DOT1L PROBE OPTIMIZATION BY LABEL-FREE LIGAND DISPLACEMENT
 
Authors :  X. Xu, S. Dhe-Paganon, S. Blacklow
Date :  06 Nov 14  (Deposition) - 03 Dec 14  (Release) - 26 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.41
Chains :  Asym./Biol. Unit :  A
Keywords :  Dot1L, Methyltransferase, Inhibitor, Leukemia, Transferase- Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. S. Yi, A. J. Federation, J. Qi, S. Dhe-Paganon, M. Hadler, X. Xu, R. St Pierre, A. C. Varca, L. Wu, J. J. Marineau, W. B. Smith, A. Souza, E. J. Chory, S. A. Armstrong, J. E. Bradner
Structure-Guided Dot1L Probe Optimization By Label-Free Ligand Displacement.
Acs Chem. Biol. V. 10 667 2015
PubMed-ID: 25397901  |  Reference-DOI: 10.1021/CB500796D

(-) 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 Taxid: 562
    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, 8)

Asymmetric/Biological Unit (4, 8)
No.NameCountTypeFull Name
13US1Ligand/IonN-[4-(ACETYLAMINO)BUTYL]-5'-[(3-{[(4-TERT-BUTYLPHENYL)CARBAMOYL]AMINO}PROPYL)(PROPAN-2-YL)AMINO]-5'-DEOXYADENOSINE
2EDO3Ligand/Ion1,2-ETHANEDIOL
3GOL1Ligand/IonGLYCEROL
4SO43Ligand/IonSULFATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:161 , LEU A:162 , GLY A:163 , SER A:164 , GLY A:165 , VAL A:169 , GLU A:186 , LYS A:187 , GLY A:221 , ASP A:222 , PHE A:223 , ASN A:241 , PHE A:245 , HOH A:529binding site for residue 3US A 401
2AC2SOFTWAREARG A:203 , LYS A:207 , HIS A:213 , HOH A:567binding site for residue SO4 A 402
3AC3SOFTWAREHIS A:117 , GLU A:201binding site for residue SO4 A 403
4AC4SOFTWAREHIS A:251 , LYS A:254 , ARG A:343binding site for residue SO4 A 404
5AC5SOFTWAREVAL A:160 , TYR A:183 , ARG A:231 , THR A:235binding site for residue GOL A 405
6AC6SOFTWAREGLU A:46 , LYS A:97 , SER A:103 , LYS A:211binding site for residue EDO A 406
7AC7SOFTWAREASN A:99 , THR A:100 , ARG A:101binding site for residue EDO A 407
8AC8SOFTWAREARG A:292 , VAL A:294binding site for residue EDO A 408

(-) SS Bonds  (0, 0)

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

(-) 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 4WVL)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4WVL)

(-) 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:331
                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee........eeee....eee..eehhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhh............hhhhhhhhhhhh......eeeee....hhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhhhhhhh.....eeeee....hhhhhhhhhh..eeee.....hhhhhhhhhhhhh......eeee.................hhhh.eeeeee...............eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4wvl A   4 KLELRLKSPVGAEPAVYPWPLPVYDKHHDAAHEIIETIRWVCEEIPDLKLAMEDYDTKSFESMQRLCDKYNRAIDSIHQLWKGTTQPMKLNTRPSTGLLRHILQQVYNHSVTDPEKLNNYGETSFDLVAQMIDEIKMTDDDLFVDLGSGVGQVVLQVAAATNCKHHYGVEKADIPAKYAETMDREFRKWMKWYGKKHAEYTLERGDFLSEEWRERIANTSVIFVNNFAFGPEVDHQLKERFANMKEGGRIVSSKPFAPLNFRINSRNLSDIGTIMRVVELSPLKGSVSWTGKPVSYYLHTIDRTILENYFSSLKNPKLREEQEAARRRQQR 347
                                    13        23        33        43        53  ||    68        78        88        98       108       118       128|      146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346 
                                                                               56|                                                               128|                                                                                                                                                                                                                  
                                                                                62                                                                137
   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  (0, 0)

(no "SCOP Domain" information available for 4WVL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)

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  4wvl
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  DOT1L_HUMAN | Q8TEK3
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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 4er3 4er5 4er6 4er7 4hra 5drt 5dry 5dsx 5dt2 5dtm 5dtq 5dtr 5juw 5mvs 5mw3 5mw4

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4WVL)