SMTL ID : 6s84.1

TsaBDE complex from Thermotoga maritima

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.89 Å

Oligo State

hetero-2-2-2-mer

Ligands

4 x APC: DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER(Non-covalent)

APC.1: 14 residues within 4Å: Chain A: S.134, G.135, G.136, H.137, G.161, D.165, G.178, P.179, D.182, G.264, V.265, A.267, N.268 Chain F: F.87 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.134, A:G.135, A:G.135, A:D.165, A:G.178, A:D.182, A:G.264 Salt bridges: A:H.137 pi-Stacking: A:F.164 APC.3: 24 residues within 4Å: Chain B: L.32, T.33, E.34, L.37, L.60, G.61, A.62, G.63, K.64, T.65, T.66, D.103, E.131, W.132, E.154, S.155, H.156, R.157 Chain C: K.166, A.210, G.211, K.213, T.214 Ligands: MG.2 19 PLIP interactions: 15 interactions with chain B, 4 interactions with chain C Hydrogen bonds: B:E.34, B:G.61, B:A.62, B:G.63, B:K.64, B:T.65, B:T.65, B:T.66, B:T.66, B:S.155, B:R.157, B:R.157, B:R.157, C:D.158, C:A.210 pi-Cation interactions: B:R.157, B:R.157 Salt bridges: C:K.166, C:K.213 APC.4: 14 residues within 4Å: Chain B: F.87 Chain C: M.132, S.134, G.135, H.137, G.161, D.165, G.178, P.179, D.182, G.264, V.265, A.267, N.268 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:S.134, C:S.134, C:G.135, C:D.165, C:G.178, C:D.182, C:G.264 Salt bridges: C:H.137 pi-Stacking: C:F.164 APC.7: 23 residues within 4Å: Chain A: D.158, K.166, A.210, G.211, K.213, T.214 Chain F: L.32, T.33, E.34, L.37, L.60, G.61, A.62, G.63, K.64, T.65, T.66, E.131, W.132, E.154, S.155, R.157 Ligands: MG.6 18 PLIP interactions: 13 interactions with chain F, 5 interactions with chain A Hydrogen bonds: F:E.34, F:G.61, F:K.64, F:K.64, F:T.65, F:T.65, F:T.66, F:E.131, F:W.132, F:S.155, A:A.210, A:K.213, A:T.214 Salt bridges: F:K.64, A:K.166, A:K.213 pi-Cation interactions: F:R.157, F:R.157

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 5 residues within 4Å: Chain B: T.65, S.84, D.103, E.131 Ligands: APC.3 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:T.65, B:E.131 MG.6: 5 residues within 4Å: Chain F: T.65, S.84, D.103, E.131 Ligands: APC.7 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:T.65, F:E.131

1 x LEU: LEUCINE(Non-covalent)

LEU.5: 3 residues within 4Å: Chain F: R.178, K.179, E.180 2 PLIP interactions: 2 interactions with chain F, Hydrophobic interactions: F:E.180 Hydrogen bonds: F:E.180

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Missoury, S. et al., The structure of the TsaB/TsaD/TsaE complex reveals an unexpected mechanism for the bacterial t6A tRNA-modification. Nucleic Acids Res. (2018)

Release Date

2019-07-17

Peptides

tRNA N6-adenosine threonylcarbamoyltransferase: AC
ATPase YjeE, predicted to have essential role in cell wall biosynthesis: BF
tRNA threonylcarbamoyladenosine biosynthesis protein TsaB: DE

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
D

B
E

F
B

D
C

E
F

tRNA N6-adenosine threonylcarbamoyltransferase

ATPase YjeE, predicted to have essential role in cell wall biosynthesis

tRNA threonylcarbamoyladenosine biosynthesis protein TsaB

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