Structure of PDB 3lhd Chain A Binding Site BS01

Receptor Information
>3lhd Chain A (length=253) Species: 272844 (Pyrococcus abyssi GE5) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MIREGDKVVLVDPRGKRYLITVSKRDFHTDLGILKLEEIIGRNFGEAIKS
HKGHEFKILRPRIVDYLDKMKRGPQIVHPKDAALIVAYAGISPGDFIVEA
GVGSGALTLFLANIVGPEGRVVSYEIREDFAKLAWENIKWAGFDDRVTIK
LKDIYEGIEEENVDHVILDLPQPERVVEHAAKALKPGGFFVAYTPCSNQV
MRLHEKLREFKDYFMKPRTINVLVFDQEVKKECMRPRTTALVHTGYITFA
RRI
Ligand information
Ligand IDSAH
InChIInChI=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
InChIKeyZJUKTBDSGOFHSH-WFMPWKQPSA-N
SMILES
SoftwareSMILES
CACTVS 3.341N[CH](CCSC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23)C(O)=O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CSCCC(C(=O)O)N)O)O)N
CACTVS 3.341N[C@@H](CCSC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)C(O)=O
ACDLabs 10.04O=C(O)C(N)CCSCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CSCC[C@@H](C(=O)O)N)O)O)N
FormulaC14 H20 N6 O5 S
NameS-ADENOSYL-L-HOMOCYSTEINE
ChEMBLCHEMBL418052
DrugBankDB01752
ZINCZINC000004228232
PDB chain3lhd Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3lhd Insights into the hyperthermostability and unusual region-specificity of archaeal Pyrococcus abyssi tRNA m1A57/58 methyltransferase.
Resolution2.59 Å
Binding residue
(original residue number in PDB)		G101 E125 I126 D153 I154 Y155 D169 L170 P171
Binding residue
(residue number reindexed from 1)		G101 E125 I126 D153 I154 Y155 D169 L170 P171
Annotation score5
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3lhd, PDBe:3lhd, PDBj:3lhd
PDBsum3lhd
PubMed20483913
UniProtQ9V1J7|TRMI_PYRAB tRNA (adenine(57)-N(1)/adenine(58)-N(1))-methyltransferase TrmI (Gene Name=trmI)

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