SMTL ID : 5ccx.1

Structure of the product complex of tRNA m1A58 methyltransferase with tRNA3Lys as substrate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

hetero-2-2-mer

Ligands

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

SAH.1: 29 residues within 4Å: Chain A: T.84, Q.85, I.86, L.87, 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 E: N.94 Chain F: U.56, C.57, A.59 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:L.87, A:S.110, A:G.111, A:T.112, A:G.113, 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:R.140, A:D.163, A:V.164, A:D.181, A:D.181 pi-Stacking: A:F.136, A:F.136 SAH.3: 29 residues within 4Å: Chain B: N.94 Chain C: U.56, C.57, A.59 Chain D: T.84, Q.85, I.86, L.87, 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 20 PLIP interactions: 20 interactions with chain D Hydrogen bonds: D:L.87, D:S.110, D:G.111, D:T.112, D:G.113, D:S.114, D:G.115, D:S.116, D:V.117, D:E.135, D:E.135, D:F.136, D:R.140, D:R.140, D:D.163, D:D.163, D:V.164, D:D.181 pi-Stacking: D:F.136, D:F.136

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

NA.2: 3 residues within 4Å: Chain C: U.9, A.10, U.13 No protein-ligand interaction detected (PLIP) NA.4: 3 residues within 4Å: Chain F: U.9, A.10, 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: AD
tRNA (adenine(58)-N(1))-methyltransferase non-catalytic subunit TRM6: BE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

D
A

B
B

E
B

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

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

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