SMTL ID : 4d7a.1 (1 other biounit)

Crystal structure of E. coli tRNA N6-threonylcarbamoyladenosine dehydratase, TcdA, in complex with AMP at 1.801 Angstroem resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

2 x K: POTASSIUM ION(Non-covalent)

K.1: 4 residues within 4Å: Chain A: Q.158, Q.174, S.206, E.208 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:Q.174, A:S.206, A:E.208 K.5: 5 residues within 4Å: Chain B: Q.158, I.173, Q.174, S.206, E.208 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:Q.174, B:S.206, B:E.208, H2O.12

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.2: 18 residues within 4Å: Chain A: V.36, G.37, I.38, G.39, G.40, I.60, D.61, D.63, R.72, Q.73, K.85, F.108, V.109, A.128, I.129, D.130, S.131, P.134 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:G.40, A:D.63, A:D.63, A:Q.73, A:K.85, A:V.109, A:V.109 Water bridges: A:G.39, A:V.41, A:R.72, A:R.72, A:S.131, A:S.131 Salt bridges: A:R.72 pi-Stacking: A:F.108, A:F.108 AMP.7: 18 residues within 4Å: Chain B: V.36, G.37, I.38, G.39, G.40, I.60, D.61, D.63, R.72, Q.73, K.85, F.108, V.109, A.128, I.129, D.130, S.131, P.134 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:I.38, B:I.38, B:G.40, B:D.63, B:D.63, B:Q.73, B:V.109, B:V.109, B:D.130 Water bridges: B:G.39, B:V.41, B:V.41, B:R.72, B:R.72, B:R.72, B:S.131, B:S.131 Salt bridges: B:R.72 pi-Stacking: B:F.108, B:F.108

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: S.254, H.255, K.258 Chain B: D.160, P.161, T.162 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:H.255, A:K.258, A:K.258, B:I.159, B:T.162 Water bridges: B:D.160, B:T.162 GOL.4: 8 residues within 4Å: Chain A: C.142, R.143, I.147, P.148, L.149, G.200, V.201, D.202 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:C.142, A:I.147, A:L.149, A:D.202 Water bridges: A:Y.124, A:K.146 GOL.8: 7 residues within 4Å: Chain B: C.142, I.147, P.148, L.149, G.200, V.201, D.202 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:C.142, B:L.149 Water bridges: B:K.146

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

NA.6: 3 residues within 4Å: Chain A: T.162, I.164 Chain B: T.162 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: 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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