SMTL ID : 4d79.1 (1 other biounit)

Crystal structure of E. coli tRNA N6-threonylcarbamoyladenosine dehydratase, TcdA, in complex with ATP at 1.768 Angstroem resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.77 Å

Oligo State

homo-dimer

Ligands

2 x K: POTASSIUM ION(Non-covalent)

K.1: 5 residues within 4Å: Chain A: Q.158, Q.174, S.206, E.208, L.210 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:Q.174, A:S.206, A:E.208 K.5: 6 residues within 4Å: Chain B: Q.158, I.173, Q.174, S.206, E.208, L.210 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:Q.174, B:S.206, B:E.208, H2O.9

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

ATP.2: 19 residues within 4Å: Chain A: V.36, G.37, I.38, G.39, G.40, I.60, D.61, D.63, N.69, R.72, Q.73, K.85, F.108, V.109, A.128, I.129, D.130, S.131, P.134 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:I.38, A:G.40, A:D.63, A:D.63, A:N.69, A:Q.73, A:K.85, A:V.109, A:V.109, A:D.130 Water bridges: A:V.41, A:V.41, A:D.63, A:D.63, A:R.72, A:R.72, A:R.72 Salt bridges: A:R.72, A:R.72, A:R.72, A:K.85 ATP.7: 18 residues within 4Å: Chain B: V.36, G.37, G.39, G.40, I.60, D.61, D.63, N.69, R.72, Q.73, K.85, D.107, F.108, V.109, A.128, I.129, D.130, P.134 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:G.40, B:N.69, B:Q.73, B:K.85, B:V.109, B:V.109, B:D.130 Water bridges: B:G.39, B:G.39, B:V.41, B:V.41, B:D.63, B:R.72, B:R.72, B:K.85 Salt bridges: B:R.72, B:R.72, B:R.72, B:K.85, B:K.85

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: V.166, S.254, H.255, K.258 Chain B: D.160, P.161, T.162 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:H.255, A:K.258, A:K.258, B:T.162 GOL.4: 7 residues within 4Å: Chain A: C.142, R.143, I.147, P.148, L.149, G.200, D.202 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:C.142, A:I.147, A:L.149, A:D.202, A:D.202 Water bridges: A:Y.124 GOL.8: 9 residues within 4Å: Chain B: C.142, R.143, I.147, P.148, L.149, G.200, V.201, D.202 Ligands: GOL.9 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:C.142, B:I.147, B:L.149, B:D.202, B:D.202 Water bridges: B:Y.124, B:K.146 GOL.9: 6 residues within 4Å: Chain B: Y.124, P.148, K.259, M.260, K.263 Ligands: GOL.8 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.124, B:K.259 Water bridges: B:Y.124

1 x NA: SODIUM ION(Non-functional Binders)

NA.6: 2 residues within 4Å: Chain A: T.162 Chain B: T.162 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.164 Water bridges: A:I.164

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lopez-Estepa, M. et al., The Crystal Structure and Small-Angle X-Ray Analysis of Csdl/Tcda Reveal a New tRNA Binding Motif in the Moeb/E1 Superfamily. Plos One (2015)

Release Date

2015-05-06

Peptides

TRNA THREONYLCARBAMOYLADENOSINE DEHYDRATASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

TRNA THREONYLCARBAMOYLADENOSINE DEHYDRATASE

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