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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN SETD2 SET-DOMAIN IN COMPLEX WITH H3K36M PEPTIDE AND SAH
 
Authors :  Y. Zhang, L. Tong
Date :  02 Mar 17  (Deposition) - 22 Mar 17  (Release) - 29 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Methyltransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Zhang, C. M. Shan, J. Wang, K. Bao, L. Tong, S. Jia
Molecular Basis For The Role Of Oncogenic Histone Mutations In Modulating H3K36 Methylation.
Sci Rep V. 7 43906 2017
PubMed-ID: 28256625  |  Reference-DOI: 10.1038/SREP43906

(-) Compounds

Molecule 1 - HISTONE-LYSINE N-METHYLTRANSFERASE SETD2
    Chains: A
    EC Number: 2.1.1.43
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: SET DOMAIN (UNP RESIDUES 1435-1711)
    Gene: SETD2, HIF1, HYPB, KIAA1732, KMT3A, SET2, HSPC069
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HIF-1,HUNTINGTIN YEAST PARTNER B,HUNTINGTIN-INTERACTING PROTEIN 1,HIP-1,HUNTINGTIN-INTERACTING PROTEIN B,LYSINE N- METHYLTRANSFERASE 3A,SET DOMAIN-CONTAINING PROTEIN 2,HSET2,P231HBP
 
Molecule 2 - HISTONE H3K36M PEPTIDE
    Chains: B
    Engineered: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
2ZN3Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:1516 , CYS A:1529 , CYS A:1533 , CYS A:1539binding site for residue ZN A 1801
2AC2SOFTWARECYS A:1499 , CYS A:1501 , CYS A:1516 , CYS A:1520binding site for residue ZN A 1802
3AC3SOFTWARECYS A:1631 , CYS A:1678 , CYS A:1680 , CYS A:1685binding site for residue ZN A 1803
4AC4SOFTWARELYS A:1560 , GLY A:1561 , TRP A:1562 , ILE A:1602 , HIS A:1603 , TYR A:1604 , TYR A:1605 , ARG A:1625 , PHE A:1626 , ASN A:1628 , HIS A:1629 , TYR A:1666 , GLN A:1676 , LYS A:1677 , CYS A:1678 , PHE A:1679 , HOH A:1936binding site for residue SAH A 1804

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5V22)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5V22)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5V22)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5V22)

(-) Exons   (0, 0)

(no "Exon" information available for 5V22)

(-) 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:245
                                                                                                                                                                                                                                                                                      
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.hhhhhhhhhhhhhhh.......ee....ee...........hhhhhhhh.......hhhhhh.........hhhhh..hhhhhh....eeeee.....eeeee........eeee...eeehhhhhhhhhhhhhhh......eeeee..eeee...eehhhhhhee.....eeeeeeee..eeeeeeee........eeee....ee.........................hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5v22 A 1447 PSCVMDDFRDPQRWKECAKQGKMPCYFDLIEENVYLTERQCECTPLSKDERAQGEIACGEDCLNRLLMIECSSRCPNGDYCSNRRFQRKQHADVEVILTEKKGWGLRAAKDLPSNTFVLEYCGEVLDHKEFKARVKEYARNKNIHYYFMALKNDEIIDATQKGNCSRFMNHSCEPNCETQKWTVNGQLRVGFFTTKLVPSGSELTFDYQFQRYGKEAQKCFCGSANCRGYLGGENRVSIRAAGGK 1703
                                  1456      1466      1476      1498      1508      1518      1528      1538      1548      1558      1568      1578      1588      1598      1608      1618      1628      1638      1648      1658      1668      1678      1688      1698     
                                                               1485|                                                                                                                                                                                                             
                                                                1498                                                                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:15
                                                
               SCOP domains --------------- SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author .....eee....... Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
                 Transcript --------------- Transcript
                5v22 B   29 APATGGVMKPHRYRP   43
                                    38
   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  (0, 0)

(no "SCOP Domain" information available for 5V22)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5V22)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5V22)

(-) Gene Ontology  (58, 62)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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  5v22
    Family and Domain Information: ProDom | SYSTERS
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  H31_HUMAN | P68431
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  SETD2_HUMAN | Q9BYW2
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  2.1.1.43
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 Related Entries

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

UniProtKB/Swiss-Prot
        H31_HUMAN | P68431: 1cs9 1ct6 1guw 1o9s 1q3l 2b2t 2b2u 2b2v 2b2w 2c1j 2c1n 2cv5 2kwj 2kwk 2l75 2lbm 2m0o 2ndf 2ndg 2oq6 2ot7 2ox0 2ri7 2uxn 2v89 2vpg 2x0l 3a1b 3afa 3avr 3ayw 3aze 3azf 3azg 3azh 3azi 3azj 3azk 3azl 3azm 3azn 3b95 3kmt 3kqi 3lqi 3lqj 3o34 3o35 3o37 3qj6 3rig 3riy 3sou 3sow 3u31 3u3d 3u4s 3u5n 3u5o 3u5p 3uee 3uef 3uig 3uii 3uik 3v43 3w96 3w97 3w98 3w99 3wa9 3waa 3wkj 3x1s 3x1t 3x1u 3x1v 3zg6 3zvy 4a0j 4a0n 4a7j 4bd3 4c1q 4f4u 4f56 4ft2 4ft4 4fwf 4hon 4i51 4l7x 4lk9 4lka 4llb 4lxl 4n4h 4qbq 4qbr 4qbs 4tn7 4u68 4up0 4uy4 4x3k 4y6l 4yhp 4yhz 4ym5 4ym6 4z0r 4z2m 5av5 5av6 5av8 5av9 5avb 5avc 5b24 5b2i 5b2j 5b31 5c11 5c13 5c3i 5cpi 5cpj 5cpk 5d6y 5dah 5fb0 5fb1 5ffv 5gse 5gsu 5gt0 5gt3 5gtc 5hjb 5hjc 5hjd 5hyn 5iql 5j3v 5j9s 5jhn 5jin 5jiy 5jj0 5jrg 5kjh 5kji 5kkl 5m5g 5svx 5svy 5t0k 5t0m 5t1g 5t1i 5t8r 5tbn 5tdr 5tdw 5v21 5va6
        SETD2_HUMAN | Q9BYW2: 2a7o 2mdc 2mdi 2mdj 4fmu 4h12 5jjy 5jlb 5jle 5lss 5lsx 5lsy 5lsz 5lt6 5lt7 5lt8 5v21

(-) Related Entries Specified in the PDB File

5v21 5V21 CONTAINS THE SAME PROTEIN COMPLEXED WITH ZN AND SAM