SMTL ID : 4rdi.2 (1 other biounit)

Crystal structure of E. coli tRNA N6-threonylcarbamoyladenosine dehydratase, TcdA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-dimer

Ligands

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 19 residues within 4Å: Chain A: V.56, G.57, I.58, G.59, G.60, I.80, D.81, D.83, N.89, R.92, Q.93, K.105, F.128, V.129, A.148, I.149, D.150, S.151, P.154 28 PLIP interactions: 28 interactions with chain A Hydrogen bonds: A:I.58, A:I.58, A:G.60, A:D.83, A:D.83, A:N.89, A:Q.93, A:K.105, A:V.129, A:V.129, A:D.150 Water bridges: A:V.61, A:V.61, A:V.61, A:D.83, A:D.83, A:N.89, A:R.92, A:R.92, A:R.92, A:K.105, A:D.150, A:S.151, A:S.151 Salt bridges: A:R.92, A:R.92, A:R.92, A:K.105 ATP.3: 19 residues within 4Å: Chain B: V.56, G.57, I.58, G.59, G.60, I.80, D.81, D.83, N.89, R.92, Q.93, K.105, F.128, V.129, A.148, I.149, D.150, S.151, P.154 22 PLIP interactions: 22 interactions with chain B Hydrogen bonds: B:I.58, B:I.58, B:G.60, B:D.83, B:D.83, B:N.89, B:Q.93, B:K.105, B:V.129, B:V.129 Water bridges: B:V.61, B:V.61, B:D.83, B:R.92, B:R.92, B:R.92, B:K.105, B:S.151 Salt bridges: B:R.92, B:R.92, B:R.92, B:K.105

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 8 residues within 4Å: Chain A: C.162, R.163, I.167, P.168, L.169, G.220, V.221, D.222 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:C.162, A:I.167, A:L.169, A:D.222 Water bridges: A:Y.144, A:K.166 GOL.4: 8 residues within 4Å: Chain B: C.162, R.163, I.167, P.168, L.169, G.220, V.221, D.222 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:C.162, B:I.167, B:L.169, B:D.222, B:D.222

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, S. et al., The Structure of Escherichia coli TcdA (Also Known As CsdL) Reveals a Novel Topology and Provides Insight into the tRNA Binding Surface Required for N(6)-Threonylcarbamoyladenosine Dehydratase Activity. J.Mol.Biol. (2015)

Release Date

2015-08-05

Peptides

tRNA threonylcarbamoyladenosine dehydratase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

tRNA threonylcarbamoyladenosine dehydratase

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