SMTL ID : 4yvk.1

Crystal Structure of H. influenzae TrmD in complex with sinefungin and tRNA variant (G36C)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-dimer

Ligands

2 x SFG: SINEFUNGIN(Non-covalent)

SFG.1: 27 residues within 4Å: Chain A: Y.106, L.107, S.108, P.109, Q.110, G.133, R.134, Y.135, E.136, G.137, W.151, S.152, I.153, G.154, Y.156, V.157, L.158, T.159, G.160, G.161, P.164 Chain B: E.188, D.189, S.190, D.197, H.200 Chain C: G.36 11 PLIP interactions: 7 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:L.107, A:Q.110, A:G.133, A:Y.135, A:I.153, A:Y.156, A:L.158, B:D.189, B:S.190, B:D.197, B:H.200 SFG.2: 22 residues within 4Å: Chain A: S.190, D.197 Chain B: Y.106, L.107, S.108, P.109, Q.110, G.133, R.134, Y.135, E.136, G.137, W.151, S.152, I.153, G.154, Y.156, V.157, L.158, G.160, G.161, P.164 15 PLIP interactions: 11 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:Y.106, B:Y.106, B:Q.110, B:G.133, B:G.133, B:Y.135, B:I.153, B:G.154, B:Y.156, B:L.158, B:G.161, A:D.197, A:D.197, A:D.197 Salt bridges: A:H.200

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ito, T. et al., Structural basis for methyl-donor-dependent and sequence-specific binding to tRNA substrates by knotted methyltransferase TrmD. Proc.Natl.Acad.Sci.USA (2015)

Release Date

2015-07-15

Peptides

tRNA (guanine-N(1)-)-methyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

tRNA (guanine-N(1)-)-methyltransferase

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