Structure of PDB 5cd1 Chain D

Receptor sequence

>5cd1D (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: D
• 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	D	G21 H22 G23 Q37 R39 H40 R62 G64 W65 H82 T84 Q85 Y88 R140 D181 I182 P183 P208 Q212 N239	G20 H21 G22 Q36 R38 H39 R61 G63 W64 H81 T83 Q84 Y87 R139 D180 I181 P182 P207 Q211 N238
BS02	SAH	D	T84 G111 S116 V117 E135 F136 R140 D163 D181 I182	T83 G110 S115 V116 E134 F135 R139 D162 D180 I181

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)