SMTL ID : 5cd1.1

Structure of an asymmetric tetramer of human tRNA m1A58 methyltransferase in a complex with SAH and tRNA3Lys

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.60 Å

Oligo State

hetero-2-2-mer

Ligands

2 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.1: 31 residues within 4Å: Chain A: T.84, Q.85, I.86, L.87, E.109, S.110, G.111, T.112, G.113, S.114, G.115, S.116, V.117, S.118, V.134, E.135, F.136, H.137, R.140, Q.162, D.163, V.164, C.165, F.179, D.181, I.182, P.183 Chain D: N.94 Chain E: U.56, C.57, A.59 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:L.87, A:S.110, A:G.111, A:T.112, A:S.114, A:G.115, A:S.116, A:V.117, A:E.135, A:E.135, A:F.136, A:R.140, A:D.163, A:V.164, A:D.181 pi-Stacking: A:F.136, A:F.136 SAH.2: 29 residues within 4Å: Chain C: T.84, Q.85, I.86, L.87, E.109, S.110, G.111, T.112, G.113, S.114, G.115, S.116, V.117, V.134, E.135, F.136, H.137, R.140, Q.162, D.163, V.164, C.165, F.179, D.181, I.182, P.183 Chain F: U.56, C.57, A.58 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:L.87, C:G.111, C:T.112, C:G.115, C:S.116, C:V.117, C:E.135, C:E.135, C:F.136, C:R.140, C:D.163, C:V.164, C:D.181 pi-Stacking: C:F.136, C:F.136

2 x NA: SODIUM ION(Non-functional Binders)

NA.3: 4 residues within 4Å: Chain E: U.9, A.10, C.12, U.13 No protein-ligand interaction detected (PLIP) NA.4: 4 residues within 4Å: Chain F: U.9, A.10, C.12, U.13 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Finer-Moore, J. et al., Crystal Structure of the Human tRNA m(1)A58 Methyltransferase-tRNA3(Lys) Complex: Refolding of Substrate tRNA Allows Access to the Methylation Target. J.Mol.Biol. (2015)

Release Date

2015-11-04

Peptides

tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A: AC
tRNA (adenine(58)-N(1))-methyltransferase non-catalytic subunit TRM6: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
D

B
B

D
E

tRNA (adenine(58)-N(1))-methyltransferase catalytic subunit TRMT61A

tRNA (adenine(58)-N(1))-methyltransferase non-catalytic subunit TRM6

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