SMTL ID : 3lga.1

Crystal structure of P. abyssi tRNA m1A58 methyltransferase in complex with S-adenosyl-L-homocysteine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

homo-tetramer

Ligands

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

SAH.1: 22 residues within 4Å: Chain A: Q.75, I.76, V.77, G.101, V.102, G.103, S.104, G.105, A.106, L.107, Y.124, E.125, I.126, R.127, F.130, K.152, D.153, I.154, Y.155, D.169, L.170, P.171 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:V.77, A:G.101, A:G.101, A:V.102, A:G.103, A:S.104, A:G.105, A:A.106, A:L.107, A:I.126, A:D.153, A:I.154, A:Y.155 Water bridges: A:T.108 SAH.3: 22 residues within 4Å: Chain B: Q.75, I.76, V.77, G.101, V.102, G.103, S.104, G.105, A.106, L.107, Y.124, E.125, I.126, R.127, F.130, K.152, D.153, I.154, Y.155, D.169, L.170, P.171 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:V.77, B:G.101, B:G.101, B:V.102, B:G.103, B:S.104, B:G.105, B:A.106, B:L.107, B:I.126, B:D.153, B:I.154, B:D.169 Water bridges: B:T.108, B:Y.155, B:Y.155 SAH.5: 22 residues within 4Å: Chain C: Q.75, I.76, V.77, G.101, V.102, G.103, S.104, G.105, A.106, L.107, Y.124, E.125, I.126, R.127, F.130, K.152, D.153, I.154, Y.155, D.169, L.170, P.171 15 PLIP interactions: 15 interactions with chain C Hydrogen bonds: C:V.77, C:G.101, C:G.101, C:G.103, C:S.104, C:G.105, C:A.106, C:L.107, C:I.126, C:D.153, C:I.154, C:D.169 Water bridges: C:T.108, C:Y.155, C:Y.155 SAH.7: 22 residues within 4Å: Chain D: Q.75, I.76, V.77, G.101, V.102, G.103, S.104, G.105, A.106, L.107, Y.124, E.125, I.126, R.127, F.130, K.152, D.153, I.154, Y.155, D.169, L.170, P.171 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:V.77, D:G.101, D:G.101, D:G.103, D:S.104, D:G.105, D:A.106, D:L.107, D:I.126, D:D.153, D:I.154 Water bridges: D:T.108

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

SO4.2: 4 residues within 4Å: Chain A: G.15, K.16, R.17, K.69 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.17 Water bridges: A:G.15, A:R.17 Salt bridges: A:R.17, A:K.69 SO4.4: 3 residues within 4Å: Chain B: K.16, R.17, K.69 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.17 Water bridges: B:R.17, B:R.17 Salt bridges: B:R.17, B:K.69 SO4.6: 3 residues within 4Å: Chain C: K.16, R.17, K.69 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.17 Water bridges: C:R.17, C:R.17 Salt bridges: C:R.17, C:K.69 SO4.8: 3 residues within 4Å: Chain D: K.16, R.17, K.69 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:R.17 Water bridges: D:G.15, D:R.17 Salt bridges: D:R.17, D:K.69

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Guelorget, A. et al., Insights into the hyperthermostability and unusual region-specificity of archaeal Pyrococcus abyssi tRNA m1A57/58 methyltransferase. Nucleic Acids Res. (2010)

Release Date

2010-06-02

Peptides

SAM-dependent methyltransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

SAM-dependent methyltransferase

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