Structure of PDB 6emv Chain C Binding Site BS01

Receptor Information

>6emv Chain C (length=169) Species: 311400 (Thermococcus kodakarensis)

PYFIIDLYHWDKHTQKEKGKIALQVNQSYGLLRDYFTELAVTWANEEFRE
MFHGPLDRITTYGGPTSEFLKENGINEVVLLDPWAEEVLSEKDFDVKAFI
IGGIVDTKKKTTPKIGEELESAGIKVRRRKIVLRGDVVGVPDRINRILGI
ILKMMVEGKSMDEAVYEMQ

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: 6emv Chain C Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6emv Structural and biochemical analysis of the dual-specificity Trm10 enzyme fromThermococcus kodakaraensisprompts reconsideration of its catalytic mechanism.
• Resolution: 2.90001 Å
• Binding residue (original residue number in PDB): L181 D182 P183 W184 G202 I204 T214 T215 K233 I234 D245 I250
• Binding residue (residue number reindexed from 1): L81 D82 P83 W84 G102 I104 T111 T112 K130 I131 D142 I147
• Annotation score: 5

Enzymatic activity

• Enzyme Commision number: 2.1.1.218: tRNA (adenine(9)-N(1))-methyltransferase.
  2.1.1.221: tRNA (guanine(9)-N(1))-methyltransferase.

External links

• PDB: RCSB:6emv, PDBe:6emv, PDBj:6emv
• PDBsum: 6emv
• PubMed: 29848639
• UniProt: Q5JD38|TRM10_THEKO tRNA (guanine(9)-/adenine(9)-N1)-methyltransferase (Gene Name=TK0422)