Structure of PDB 5cd1 Chain A

Receptor sequence

>5cd1A (length=281) Species: 9606 (Homo sapiens)

SFVAYEELIKEGDTAILSLGHGAMVAVRVQRGAQTQTRHGVLRHSVDLIG
RPFGSKVTCGRGGWVYVLHPTPELWTLNLPHRTQILYSTDIALITMMLEL
RPGSVVCESGTGSGSVSHAIIRTIAPTGHLHTVEFHQQRAEKAREEFQEH
RVGRWVTVRTQDVCRSGFGVSHVADAVFLDIPSPWEAVGHAWDALKVEGG
RFCSFSPCIEQVQRTCQALAARGFSELSTLEVLPQVYNVRTVSLPPPDLG
TGDTSPFRSGTPMKEAVGHTGYLTFATKTPG

3D structure

• PDB: 5cd1 Crystal Structure of the Human tRNA m(1)A58 Methyltransferase-tRNA3(Lys) Complex: Refolding of Substrate tRNA Allows Access to the Methylation Target.
• Chain: A
• Resolution: 3.6 Å

Enzymatic activity

• Enzyme Commision number: 2.1.1.-
  2.1.1.220: tRNA (adenine(58)-N(1))-methyltransferase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	rna	A	G21 H22 Q37 T38 H40 G64 W65 H82 T84 Q85 L87 D181 I182 P183 F206 P208 C209 Q212	G20 H21 Q36 T37 H39 G63 W64 H81 T83 Q84 L86 D180 I181 P182 F205 P207 C208 Q211
BS02	SAH	A	T84 Q85 I86 S110 G111 S116 V117 E135 F136 R140 V164 D181 I182 P183	T83 Q84 I85 S109 G110 S115 V116 E134 F135 R139 V163 D180 I181 P182

Gene Ontology

Molecular Function

• GO:0005515 protein binding
• GO:0008168 methyltransferase activity
• GO:0061953 mRNA (adenine-N1-)-methyltransferase activity
• GO:0160107 tRNA (adenine(58)-N1)-methyltransferase activity

Biological Process

• GO:0006397 mRNA processing
• GO:0008033 tRNA processing
• GO:0030488 tRNA methylation
• GO:0032259 methylation

Cellular Component

• GO:0005634 nucleus
• GO:0005654 nucleoplasm
• GO:0031515 tRNA (m1A) methyltransferase complex

External links

• PDB: RCSB:5cd1, PDBe:5cd1, PDBj:5cd1
• PDBsum: 5cd1
• PubMed: 26470919
• UniProt: Q96FX7|TRM61_HUMAN tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A (Gene Name=TRMT61A)