Structure of PDB 5kkl Chain B Binding Site BS09

Receptor Information

>5kkl Chain B (length=839) Species: 9606,759272

WTVDKIASALSVLAEEVPQNHSRLVNFLLEETEKRAPQPRHLSKTDPFAH
MKSKAVPTMDVKFKQHSGEYGKSRNSGRRFQYPVVCIKPDREPVPPYRFH
HAEIRKNILALNSQLNFVPHLRDVDPNSAEEQKYSAWLMDLENLDSKSGF
KIQPRSQKIAKRAQAEYAATLAPYLEPWLRKLNIEGCTKSNLIRFMASQP
DSMTPQQKSNLLDTYSDDMGSPQAVRNASMFTEAWDRVFNDQSKLRRVAL
RDILMLDKNVEPIFDNKRAKEALMQKVIDALGSYTTLGCLICFSHDCEHG
EIERDNQKRCFSLEEIGGLMPSLRRKWAAQIEQRQKTPPCRNECYRIHGT
GDPNQQVPPWSENEVGTLEWMFATIGYSQTLRPECFVGAILGRPCWDVHR
KLQELDLRLPPVEPRTIPKQKSLPWYDRRKKQLMSDWADATITHEHAVRE
LFAPCHHDGPCTAANGCPCASAGTHPVLCERFCLCTAEECPLKFTGCACH
SSGKTCLQRQGRPCICVQLNRECDPTLCKGCGARERADPENAYDEVLHST
GCQNVALQRGAAKAVVLGKSQLEACGYGLFAAEDIEEGEFVIEYTGELIS
HDEGVRREHRRGDVFDKVSYLFTLLEQEGIWVDAAIYGNLSRYINHATDG
NIMPKIMYVNHEWRIKFTAIKDIKAGEELFFNYGDNFPNLTKTKAARMSA
PKPLLVPKTTQPLFDPLSKVQLLPGQPLPQHPIDDSWLLLKHRDNLQDFI
DLRPEEKEFLQEWDAFILRRHISSEQYLPRYFLRFVREKADWLVSKRSRG
EEFSKLVATLLARRVLPERVVIEATQVLNDARGRLREQG

Ligand information

• Ligand ID: SAM
• InChI: InChI=1S/C15H22N6O5S/c1-27(3-2-7(16)15(24)25)4-8-10(22)11(23)14(26-8)21-6-20-9-12(17)18-5-19-13(9)21/h5-8,10-11,14,22-23H,2-4,16H2,1H3,(H2-,17,18,19,24,25)/t7-,8+,10+,11+,14+,27-/m0/s1
• InChIKey: MEFKEPWMEQBLKI-FCKMPRQPSA-N
• SMILES:
  CACTVS 3.341: C[S@@+](CC[C@H](N)C([O-])=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
  OpenEye OEToolkits 1.5.0: C[S+](CCC(C(=O)[O-])N)CC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
  CACTVS 3.341: C[S+](CC[CH](N)C([O-])=O)C[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
  OpenEye OEToolkits 1.5.0: C[S@@+](CC[C@@H](C(=O)[O-])N)C[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O
  ACDLabs 10.04: [O-]C(=O)C(N)CC[S+](C)CC3OC(n2cnc1c(ncnc12)N)C(O)C3O
• Formula: C15 H22 N6 O5 S
• Name: S-ADENOSYLMETHIONINE
• ChEMBL: CHEMBL1235831
• PDB chain: 5kkl Chain B Residue 8009

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5kkl Response to Comment on "Structural basis of histone H3K27 trimethylation by an active polycomb repressive complex 2".
• Resolution: 2.94 Å
• Binding residue (original residue number in PDB): C807 G808 Y809 S854 Y855 R877 Y878 N880 H881 Y918 F922 L925 T926 M2027
• Binding residue (residue number reindexed from 1): C575 G576 Y577 S619 Y620 R642 Y643 N645 H646 Y683 F687 L690 T691 M698
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): Y826 Y918
• Catalytic site (residue number reindexed from 1): Y594 Y683

Gene Ontology

Molecular Function

• GO:0042054 histone methyltransferase activity

Biological Process

• GO:0006338 chromatin remodeling

External links

• PDB: RCSB:5kkl, PDBe:5kkl, PDBj:5kkl
• PDBsum: 5kkl
• PubMed: 28008038
• UniProt: G0RYC6;
  G0SDW4;
  P68431|H31_HUMAN Histone H3.1 (Gene Name=H3C1)