SMTL ID : 4yqd.1

Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

homo-dimer

Ligands

2 x 4GZ: 6-{[(1-{2-[(3-methylbenzoyl)amino]ethyl}cyclohexyl)methyl]amino}pyridine-3-carboxamide(Non-covalent)

4GZ.1: 22 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, S.152, I.153, G.154, Y.156, V.157, L.158, G.160, G.161, P.164 Chain B: A.184, L.195, D.197 13 PLIP interactions: 10 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:Y.106, A:V.157, A:P.164, B:A.184, B:D.197 Hydrogen bonds: A:Q.110, A:I.153, A:G.154, A:Y.156, A:L.158, A:L.158, B:D.197 Water bridges: A:E.136 4GZ.2: 22 residues within 4Å: Chain A: A.184, L.195, D.197 Chain B: Y.106, L.107, S.108, P.109, Q.110, G.133, R.134, Y.135, E.136, G.137, S.152, I.153, G.154, Y.156, V.157, L.158, G.160, G.161, P.164 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:Y.106, B:V.157, B:P.164, A:A.184, A:D.197 Hydrogen bonds: B:Q.110, B:I.153, B:G.154, B:Y.156, B:L.158, B:L.158

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Elkins, P.A. et al., Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds. To be published

Release Date

2015-11-11

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

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

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