Structure of PDB 5kjh Chain B Binding Site BS10

Receptor Information

>5kjh Chain B (length=807) Species: 759272 (Thermochaetoides thermophila DSM 1495)

WTVDKIASALSVLAEEVPQNHSRLVNFLLEETEKRAPQPRHLSKTDPFAH
MKSKAIDANRPRPEGVPTMDVKFKQHSGEYGKSRNSGRRFQYPVVCIKPD
REPVPPYRFHHAEIRKNILALNSQLNFVPHLRDVDPNSAEEQKYSAWLMD
LENLDSKSGFPRSQKIAKRAQAEYAATLAPYLEPWLRKLNIECTKSNLIR
FMASQPETPQQKSNLLDTYSDDAVRNASMFTEAWDRVFNDQRRVALRDIL
MLDKNVEPIFEALMQKVIDALGSYTTLGCLICFSHDCEHGEIERDNQKRC
FSLEEIGGLMPSLRRKWAAQIEQPPCRNECYIHGTPPWSENEVGTLEWMF
ATIGYSLRPECFVGAILRPCWDVHRKLQELDLRLPIPKQKSLPWYDRRKK
QLMSDWADATITHEHAVRELFAPCHHDGPCTAANGCPCASAGTHPVLCER
FCLCTAEECPLKFTGCACHSSGKTCLQRQGRPCICVQLNRECDPTLCKGC
GARERADPENAYDEVLHSTGCQNVALQRGAAKAVVLGKSQLEACGYGLFA
AEDIEEGEFVIEYTGELISHDEGVRREHRRGDVFDKVSYLFTLLEQEGIW
VDAAIYGNLSRYINHATDGNIMPKIMYVNHEWRIKFTAIKDIKAGEELFF
NYGDNFPNLTKKLEVMLPGRGVPPLLVPKTTQPLFDPLSKVQLLPGQPLP
QHPIDDSWLLLKHRDNLQDFIDLRPEEKEFLQEWDAFILRRHISSEQYLP
RYFLRFVREKADWLVSKRSRGEEFSKLVATLLARRVLPERVVIEATQVLN
DARGRLR

Ligand information

• Ligand ID: SAH
• InChI: InChI=1S/C14H20N6O5S/c15-6(14(23)24)1-2-26-3-7-9(21)10(22)13(25-7)20-5-19-8-11(16)17-4-18-12(8)20/h4-7,9-10,13,21-22H,1-3,15H2,(H,23,24)(H2,16,17,18)/t6-,7+,9+,10+,13+/m0/s1
• InChIKey: ZJUKTBDSGOFHSH-WFMPWKQPSA-N
• SMILES:
  CACTVS 3.341: N[CH](CCSC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23)C(O)=O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CSCCC(C(=O)O)N)O)O)N
  CACTVS 3.341: N[C@@H](CCSC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)C(O)=O
  ACDLabs 10.04: O=C(O)C(N)CCSCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CSCC[C@@H](C(=O)O)N)O)O)N
• Formula: C14 H20 N6 O5 S
• Name: S-ADENOSYL-L-HOMOCYSTEINE
• ChEMBL: CHEMBL418052
• DrugBank: DB01752
• ZINC: ZINC000004228232
• PDB chain: 5kjh Chain B Residue 8009

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5kjh Response to Comment on "Structural basis of histone H3K27 trimethylation by an active polycomb repressive complex 2".
• Resolution: 2.27 Å
• Binding residue (original residue number in PDB): C807 G808 Y809 K852 V853 S854 Y855 R877 N880 H881 Y918 F922 L925 K927 R2536
• Binding residue (residue number reindexed from 1): C544 G545 Y546 K586 V587 S588 Y589 R611 N614 H615 Y652 F656 L659 K661 R670
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): Y826 Y918
• Catalytic site (residue number reindexed from 1): Y563 Y652

Gene Ontology

Molecular Function

• GO:0042054 histone methyltransferase activity

Biological Process

• GO:0006338 chromatin remodeling

External links

• PDB: RCSB:5kjh, PDBe:5kjh, PDBj:5kjh
• PDBsum: 5kjh
• PubMed: 28008038
• UniProt: G0RYC6;
  G0SDW4