SMTL ID : 3mb5.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

4 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.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 17 PLIP interactions: 17 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:D.153, A:I.154 Water bridges: A:T.108, A:Y.155, A:Y.155 Salt bridges: A:D.169 SAM.13: 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 17 PLIP interactions: 17 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:D.153, B:I.154 Water bridges: B:T.108, B:Y.155, B:Y.155 Salt bridges: B:D.169 SAM.25: 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:V.102, 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 Salt bridges: C:D.169 SAM.37: 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 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:V.77, D:G.101, D:G.101, D:V.102, D:G.103, D:S.104, D:G.105, D:A.106, D:L.107, D:I.126, D:D.153, D:I.154, D:D.169 Water bridges: D:T.108 Salt bridges: D:D.169

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

SO4.2: 3 residues within 4Å: Chain A: K.16, R.17, K.69 Ligand excluded by PLIP SO4.3: 1 residues within 4Å: Chain A: K.49 Ligand excluded by PLIP SO4.4: 4 residues within 4Å: Chain A: P.13, R.14, L.31, H.54 Ligand excluded by PLIP SO4.5: 1 residues within 4Å: Chain A: R.42 Ligand excluded by PLIP SO4.14: 3 residues within 4Å: Chain B: K.16, R.17, K.69 Ligand excluded by PLIP SO4.15: 1 residues within 4Å: Chain B: K.49 Ligand excluded by PLIP SO4.16: 4 residues within 4Å: Chain B: P.13, R.14, L.31, H.54 Ligand excluded by PLIP SO4.17: 1 residues within 4Å: Chain B: R.42 Ligand excluded by PLIP SO4.26: 3 residues within 4Å: Chain C: K.16, R.17, K.69 Ligand excluded by PLIP SO4.27: 1 residues within 4Å: Chain C: K.49 Ligand excluded by PLIP SO4.28: 4 residues within 4Å: Chain C: P.13, R.14, L.31, H.54 Ligand excluded by PLIP SO4.29: 1 residues within 4Å: Chain C: R.42 Ligand excluded by PLIP SO4.38: 3 residues within 4Å: Chain D: K.16, R.17, K.69 Ligand excluded by PLIP SO4.39: 1 residues within 4Å: Chain D: K.49 Ligand excluded by PLIP SO4.40: 4 residues within 4Å: Chain D: P.13, R.14, L.31, H.54 Ligand excluded by PLIP SO4.41: 1 residues within 4Å: Chain D: R.42 Ligand excluded by PLIP

24 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 6 residues within 4Å: Chain A: F.189, M.215, K.216, F.249, A.250, R.251 Ligand excluded by PLIP EDO.7: 3 residues within 4Å: Chain A: H.78, L.241 Chain D: R.218 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: L.67, D.68, P.79, F.110 Chain D: A.87 Ligand excluded by PLIP EDO.9: 8 residues within 4Å: Chain A: I.63, F.110, N.113, I.114 Chain D: V.86, G.90, I.91, S.92 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: A.131, K.132, W.135, I.149, L.151 Ligand excluded by PLIP EDO.11: 8 residues within 4Å: Chain A: L.67, V.77, H.78, P.79, A.82, A.106, L.107, F.110 Ligand excluded by PLIP EDO.18: 6 residues within 4Å: Chain B: F.189, M.215, K.216, F.249, A.250, R.251 Ligand excluded by PLIP EDO.19: 3 residues within 4Å: Chain B: H.78, L.241 Chain C: R.218 Ligand excluded by PLIP EDO.20: 5 residues within 4Å: Chain B: L.67, D.68, P.79, F.110 Chain C: A.87 Ligand excluded by PLIP EDO.21: 8 residues within 4Å: Chain B: I.63, F.110, N.113, I.114 Chain C: V.86, G.90, I.91, S.92 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain B: A.131, K.132, W.135, I.149, L.151 Ligand excluded by PLIP EDO.23: 8 residues within 4Å: Chain B: L.67, V.77, H.78, P.79, A.82, A.106, L.107, F.110 Ligand excluded by PLIP EDO.30: 6 residues within 4Å: Chain C: F.189, M.215, K.216, F.249, A.250, R.251 Ligand excluded by PLIP EDO.31: 3 residues within 4Å: Chain B: R.218 Chain C: H.78, L.241 Ligand excluded by PLIP EDO.32: 5 residues within 4Å: Chain B: A.87 Chain C: L.67, D.68, P.79, F.110 Ligand excluded by PLIP EDO.33: 8 residues within 4Å: Chain B: V.86, G.90, I.91, S.92 Chain C: I.63, F.110, N.113, I.114 Ligand excluded by PLIP EDO.34: 5 residues within 4Å: Chain C: A.131, K.132, W.135, I.149, L.151 Ligand excluded by PLIP EDO.35: 8 residues within 4Å: Chain C: L.67, V.77, H.78, P.79, A.82, A.106, L.107, F.110 Ligand excluded by PLIP EDO.42: 6 residues within 4Å: Chain D: F.189, M.215, K.216, F.249, A.250, R.251 Ligand excluded by PLIP EDO.43: 3 residues within 4Å: Chain A: R.218 Chain D: H.78, L.241 Ligand excluded by PLIP EDO.44: 5 residues within 4Å: Chain A: A.87 Chain D: L.67, D.68, P.79, F.110 Ligand excluded by PLIP EDO.45: 8 residues within 4Å: Chain A: V.86, G.90, I.91, S.92 Chain D: I.63, F.110, N.113, I.114 Ligand excluded by PLIP EDO.46: 5 residues within 4Å: Chain D: A.131, K.132, W.135, I.149, L.151 Ligand excluded by PLIP EDO.47: 8 residues within 4Å: Chain D: L.67, V.77, H.78, P.79, A.82, A.106, L.107, F.110 Ligand excluded by PLIP

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.12: 3 residues within 4Å: Chain A: P.186 Chain D: F.44, R.60 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Water bridges: A:K.185 Salt bridges: A:K.185, D:R.60 ACT.24: 3 residues within 4Å: Chain B: P.186 Chain C: F.44, R.60 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Water bridges: B:K.185 Salt bridges: B:K.185, C:R.60 ACT.36: 3 residues within 4Å: Chain B: F.44, R.60 Chain C: P.186 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain C Salt bridges: B:R.60, C:K.185 Water bridges: C:K.185 ACT.48: 3 residues within 4Å: Chain A: F.44, R.60 Chain D: P.186 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain A Water bridges: D:K.185 Salt bridges: D:K.185, A:R.60

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

2010-05-12

Peptides

SAM-dependent methyltransferase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

SAM-dependent methyltransferase