SMTL ID : 2pwy.1

Crystal Structure of a m1A58 tRNA methyltransferase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-tetramer

Ligands

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 3 residues within 4Å: Chain A: F.216, R.217, L.218 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.216, A:L.218 Water bridges: A:R.217 SO4.2: 1 residues within 4Å: Chain A: R.52 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.52 SO4.5: 4 residues within 4Å: Chain B: R.254, W.255, K.256, G.257 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.257 Water bridges: B:A.185, B:R.254 Salt bridges: B:R.254 SO4.6: 3 residues within 4Å: Chain C: F.216, R.217, L.218 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:F.216, C:L.218 Water bridges: C:R.217 SO4.7: 1 residues within 4Å: Chain C: R.52 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.52 SO4.10: 4 residues within 4Å: Chain D: R.254, W.255, K.256, G.257 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:G.257 Water bridges: D:A.185, D:R.254 Salt bridges: D:R.254

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

SAH.3: 23 residues within 4Å: Chain A: A.77, T.78, P.79, T.80, G.104, T.105, G.106, S.107, G.108, G.109, L.110, Y.127, E.128, A.129, R.130, H.133, G.155, K.156, L.157, E.158, D.173, L.174, V.180 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:T.80, A:T.80, A:T.80, A:G.104, A:T.105, A:G.106, A:S.107, A:G.108, A:G.109, A:L.110, A:A.129, A:H.133, A:L.157, A:E.158, A:D.173 Water bridges: A:T.111, A:M.175 SAH.4: 21 residues within 4Å: Chain B: A.77, T.78, P.79, T.80, G.104, T.105, G.106, S.107, G.108, G.109, L.110, E.128, A.129, R.130, H.133, G.155, K.156, L.157, E.158, D.173, L.174 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:T.80, B:T.80, B:T.80, B:G.104, B:T.105, B:G.106, B:S.107, B:G.108, B:G.109, B:L.110, B:A.129, B:H.133, B:L.157, B:E.158, B:D.173 Water bridges: B:T.111, B:M.175 SAH.8: 23 residues within 4Å: Chain C: A.77, T.78, P.79, T.80, G.104, T.105, G.106, S.107, G.108, G.109, L.110, Y.127, E.128, A.129, R.130, H.133, G.155, K.156, L.157, E.158, D.173, L.174, V.180 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:T.80, C:T.80, C:G.104, C:T.105, C:G.106, C:S.107, C:G.108, C:G.109, C:L.110, C:A.129, C:H.133, C:L.157, C:E.158 Water bridges: C:T.111, C:M.175 SAH.9: 21 residues within 4Å: Chain D: A.77, T.78, P.79, T.80, G.104, T.105, G.106, S.107, G.108, G.109, L.110, E.128, A.129, R.130, H.133, G.155, K.156, L.157, E.158, D.173, L.174 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:T.80, D:T.80, D:G.104, D:T.105, D:G.106, D:S.107, D:G.108, D:G.109, D:L.110, D:A.129, D:H.133, D:L.157, D:E.158 Water bridges: D:T.111, D:M.175

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Barraud, P. et al., Crystal Structure of Thermus thermophilus tRNA m(1)A(58) Methyltransferase and Biophysical Characterization of Its Interaction with tRNA. J.Mol.Biol. (2008)

Release Date

2008-02-26

Peptides

tRNA (adenine-N(1)-)-methyltransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

tRNA (adenine-N(1)-)-methyltransferase