SMTL ID : 1v2x.1

TrmH

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 8 residues within 4Å: Chain A: K.32, H.34, N.35, E.124, N.152 Chain B: R.41, E.65, T.66 10 PLIP interactions: 7 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:N.35, B:R.41, B:E.65, B:E.65 Water bridges: A:E.124, A:E.124, A:N.152, A:V.153 Salt bridges: A:K.32, A:H.34 PO4.2: 4 residues within 4Å: Chain A: N.29, H.31, N.55, G.58 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:N.29, A:N.55, A:N.55, A:G.58 Water bridges: A:H.31 Salt bridges: A:H.31 PO4.4: 8 residues within 4Å: Chain A: R.41, E.65, T.66 Chain B: K.32, H.34, N.35, E.124, N.152 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.35, A:R.41, A:E.65 Water bridges: B:E.124, B:E.124, B:N.152, B:V.153 Salt bridges: B:K.32, B:H.34 PO4.5: 4 residues within 4Å: Chain B: N.29, H.31, N.55, G.58 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:N.29, B:N.55, B:N.55, B:G.58 Water bridges: B:H.31 Salt bridges: B:H.31

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

SAM.3: 17 residues within 4Å: Chain A: T.99, L.101, F.121, G.122, A.123, E.124, K.125, W.126, G.127, K.141, I.142, M.144, S.150, L.151, V.153, A.156 Chain B: R.41 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:T.99, A:G.122, A:G.122, A:K.125, A:I.142, A:I.142, A:L.151 Water bridges: A:Q.149, A:S.150 SAM.6: 17 residues within 4Å: Chain A: R.41 Chain B: T.99, L.101, F.121, G.122, A.123, E.124, K.125, W.126, G.127, K.141, I.142, M.144, S.150, L.151, V.153, A.156 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:G.122, B:G.122, B:K.125, B:I.142, B:I.142, B:L.151 Water bridges: B:Q.149, B:S.150

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nureki, O. et al., Deep Knot Structure for Construction of Active Site and Cofactor Binding Site of tRNA Modification Enzyme. STRUCTURE (2004)

Release Date

2004-05-04

Peptides

tRNA (Gm18) methyltransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

tRNA (Gm18) methyltransferase