Structure of PDB 3mb5 Chain A Binding Site BS01

Receptor Information

>3mb5 Chain A (length=255) Species: 29292 (Pyrococcus abyssi)

MIREGDKVVLVDPRGKRYLITVSKRDFHTDLGILKLEEIIGRNFGEAIKS
HKGHEFKILRPRIVDYLDKMKRGPQIVHPKDAALIVAYAGISPGDFIVEA
GVGSGALTLFLANIVGPEGRVVSYEIREDFAKLAWENIKWAGFDDRVTIK
LKDIYEGIEEENVDHVILDLPQPERVVEHAAKALKPGGFFVAYTPCSNQV
MRLHEKLREFKDYFMKPRTINVLVFDQEVKKECMRPRTTALVHTGYITFA
RRILE

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: 3mb5 Chain A Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3mb5 Insights into the hyperthermostability and unusual region-specificity of archaeal Pyrococcus abyssi tRNA m1A57/58 methyltransferase.
• Resolution: 1.6 Å
• Binding residue (original residue number in PDB): Q75 I76 V77 G101 G103 S104 A106 L107 E125 I126 D153 I154 Y155 D169
• Binding residue (residue number reindexed from 1): Q75 I76 V77 G101 G103 S104 A106 L107 E125 I126 D153 I154 Y155 D169
• Annotation score: 5

Enzymatic activity

• Enzyme Commision number: 2.1.1.219: tRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase.

Gene Ontology

Molecular Function

• GO:0008168 methyltransferase activity
• GO:0016740 transferase activity
• GO:0043827 tRNA (adenine(57)-N1)/(adenine(58)-N1)-methyltransferase activity
• GO:0160107 tRNA (adenine(58)-N1)-methyltransferase activity

Biological Process

• GO:0008033 tRNA processing
• GO:0030488 tRNA methylation
• GO:0032259 methylation

Cellular Component

• GO:0031515 tRNA (m1A) methyltransferase complex

External links

• PDB: RCSB:3mb5, PDBe:3mb5, PDBj:3mb5
• PDBsum: 3mb5
• PubMed: 20483913
• UniProt: Q9V1J7|TRMI_PYRAB tRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI (Gene Name=trmI)