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(-) Description

Title :  SETDB1 IN COMPLEX WITH AN EARLY STAGE, LOW AFFINITY FRAGMENT CANDIDATE MODELLED AT REDUCED OCCUPANCY
 
Authors :  W. Tempel, R. J. Harding, P. Mader, E. Dobrovetsky, J. R. Walker, P. J. Br M. Schapira, P. Collins, N. Pearce, J. Brandao-Neto, A. Douangamath, Delft, C. Bountra, C. H. Arrowsmith, A. M. Edwards, V. Santhakumar, St Genomics Consortium (Sgc)
Date :  06 Jun 16  (Deposition) - 27 Jul 16  (Release) - 27 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.47
Chains :  Asym./Biol. Unit :  A
Keywords :  Fragment Screening, Diamond I04-1 Xchem, Pandda, Structural Genomics, Structural Genomics Consortium, Sgc, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Tempel, R. J. Harding, P. Mader, E. Dobrovetsky, J. R. Walker, P. J. Brown, M. Schapira, C. H. Arrowsmith, A. M. Edwards, S. Santhakumar, Structural Genomics Consortium (Sgc)
Setdb1 In Complex With An Early Stage, Low Affinity Fragmen Candidate Modelled At Reduced Occupancy
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HISTONE-LYSINE N-METHYLTRANSFERASE SETDB1
    Chains: A
    EC Number: 2.1.1.43
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28-MHL
    Expression System Strain: BL21 (DE3) CODON PLUS
    Expression System Taxid: 469008
    Fragment: UNP RESIDUES 196-403
    Gene: SETDB1, KIAA0067, KMT1E
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ERG-ASSOCIATED PROTEIN WITH SET DOMAIN,ESET,HISTONE H3-K9 METHYLTRANSFERASE 4,H3-K9-HMTASE 4,LYSINE N-METHYLTRANSFERASE 1E,SET DOMAIN BIFURCATED 1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 53)

Asymmetric/Biological Unit (4, 53)
No.NameCountTypeFull Name
16RO1Ligand/Ion~{N}-(4-CHLOROPHENYL)METHANESULFONAMIDE
2DMS3Ligand/IonDIMETHYL SULFOXIDE
3SO42Ligand/IonSULFATE ION
4UNX47Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:214 , LYS A:215 , HOH A:612 , HOH A:634 , HOH A:639binding site for residue SO4 A 501
2AC2SOFTWAREARG A:209 , TRP A:363 , LYS A:364 , ASP A:381 , HOH A:614binding site for residue SO4 A 502
3AC3SOFTWAREPHE A:296 , GLY A:300 , ALA A:302 , SER A:328 , PHE A:332 , TYR A:389 , SER A:392 , HOH A:655binding site for residue 6RO A 503
4AC4SOFTWARELYS A:207 , LYS A:208 , LYS A:211 , HOH A:652binding site for residue DMS A 551
5AC5SOFTWARETRP A:358 , TRP A:363 , PHE A:379 , ASP A:382 , ARG A:384 , HOH A:609 , HOH A:672binding site for residue DMS A 552
6AC6SOFTWAREGLU A:190 , ASN A:191 , THR A:223binding site for residue DMS A 553

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5KCO)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Tyr A:340 -Pro A:341

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5KCO)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5KCO)

(-) Exons   (0, 0)

(no "Exon" information available for 5KCO)

(-) 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:212
                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.ee..ee...eeeee.....eeeeeeeeeeee..eeeeeeee....eeeehhh.eee....hhhhh....eeeeeeee..eeeeeeeeeee.........eeeee....eeeehhh.eee......hhhhhh.hhhhhhhhhhhhhhh............eeeeee..eeeeeeeeeee..eeeeee....eeeeee.....hhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5kco A 190 ENLYFQGDLIVSMRILGKKRTKTWHKGTLIAIQTVGPGKKYKVKFDNKGKSLLSGNHIAYDYHPPADKLYVGSRVVAKYKDGNQVWLYAGIVAETPNVKNKLRFLIFFDDGYASYVTQSELYPICRPLKKTWEDIEDISCRDFIEEYVTAYPNRPMVLLKSGQLIKTEWEGTWWKSRVEEVDGSLVRILFLDDKRCEWIYRGSTRLEPMFSM 401
                                   199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399
   Legend:   → Mismatch (orange background)
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    → 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  (0, 0)

(no "SCOP Domain" information available for 5KCO)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5KCO)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5KCO)

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Tyr A:340 - Pro A:341   [ RasMol ]  
 

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  5kco
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  SETB1_HUMAN | Q15047
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 Related Entries

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

UniProtKB/Swiss-Prot
        SETB1_HUMAN | Q15047: 3dlm 4x3s 5kch 5ke2 5ke3 5kh6

(-) Related Entries Specified in the PDB File

5kch