SMTL ID : 3axs.1

Complex structure of tRNA methyltransferase Trm1 from Aquifex aeolicus with sinefungin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.16 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.247, C.250, C.266, C.269 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.247, A:C.250, A:C.266, A:C.269 ZN.8: 4 residues within 4Å: Chain B: C.247, C.250, C.266, C.269 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.247, B:C.250, B:C.266, B:C.269

2 x SFG: SINEFUNGIN(Non-covalent)

SFG.2: 16 residues within 4Å: Chain A: R.36, L.60, S.61, A.62, I.65, R.66, N.83, D.84, I.85, S.86, M.112, E.113, A.114, D.132, F.134, F.140 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:A.62 Hydrogen bonds: A:L.60, A:A.62, A:I.85, A:E.113, A:E.113, A:A.114, A:D.132, A:D.132, A:D.132 Water bridges: A:R.36, A:R.36, A:R.36, A:R.66 Salt bridges: A:R.36, A:R.66 SFG.9: 16 residues within 4Å: Chain B: R.36, L.60, S.61, A.62, I.65, R.66, N.83, D.84, I.85, S.86, M.112, E.113, A.114, D.132, F.134, F.140 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:A.62 Hydrogen bonds: B:L.60, B:A.62, B:I.85, B:E.113, B:A.114, B:D.132, B:D.132 Water bridges: B:R.36, B:R.36, B:R.36, B:R.66 Salt bridges: B:R.36, B:R.66

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

SO4.3: 5 residues within 4Å: Chain A: S.21, S.22, R.31, L.218, H.219 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.22, A:S.22, A:H.219 Salt bridges: A:R.31 SO4.4: 3 residues within 4Å: Chain A: A.162, Y.168, H.219 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.168 Salt bridges: A:H.219 SO4.5: 4 residues within 4Å: Chain A: Y.168, P.169, K.170, T.171 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.170, A:T.171, A:T.171 Water bridges: A:R.174 SO4.6: 3 residues within 4Å: Chain A: H.110, G.111, M.112 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.111 Salt bridges: A:H.110 SO4.7: 2 residues within 4Å: Chain A: K.305, R.309 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.305, A:R.309 SO4.10: 5 residues within 4Å: Chain B: S.21, S.22, R.31, L.218, H.219 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.22, B:S.22, B:H.219 Salt bridges: B:R.31 SO4.11: 3 residues within 4Å: Chain B: A.162, Y.168, H.219 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:H.219 SO4.12: 4 residues within 4Å: Chain B: Y.168, P.169, K.170, T.171 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.170, B:T.171 Water bridges: B:R.174 SO4.13: 3 residues within 4Å: Chain B: H.110, G.111, M.112 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.111 Salt bridges: B:H.110 SO4.14: 2 residues within 4Å: Chain B: K.305, R.309 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.305, B:R.309

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Awai, T. et al., Substrate tRNA recognition mechanism of a multisite-specific tRNA methyltransferase, Aquifex aeolicus Trm1, based on the X-ray crystal structure. J.Biol.Chem. (2011)

Release Date

2011-08-03

Peptides

Probable N(2),N(2)-dimethylguanosine tRNA methyltransferase Trm1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Probable N(2),N(2)-dimethylguanosine tRNA methyltransferase Trm1

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