SMTL ID : 3fi0.3 (8 other biounits)

Crystal Structure Analysis of B. stearothermophilus Tryptophanyl-tRNA Synthetase Complexed with Tryptophan, AMP, and Inorganic Phosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

2 x TRP: TRYPTOPHAN(Non-covalent)

TRP.1: 12 residues within 4Å: Chain A: F.5, G.7, Q.9, V.40, H.43, M.129, D.132, I.133, V.141, V.143, Q.147 Ligands: AMP.3 12 PLIP interactions: 10 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:F.5, A:F.5, A:D.132, A:I.133, A:V.141, A:V.143 Hydrogen bonds: A:D.132, A:D.132, A:Q.147, A:Q.147, W.1, W.1 TRP.4: 12 residues within 4Å: Chain B: F.5, G.7, Q.9, V.40, H.43, M.129, D.132, I.133, V.141, V.143, Q.147 Ligands: AMP.6 11 PLIP interactions: 9 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: B:F.5, B:F.5, B:I.133, B:V.141, B:V.143 Hydrogen bonds: B:D.132, B:D.132, B:Q.147, B:Q.147, W.4, W.4

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

PO4.2: 5 residues within 4Å: Chain A: M.193, S.194, K.195, S.196 Ligands: AMP.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.194, A:S.194, A:K.195, A:S.196 PO4.5: 4 residues within 4Å: Chain B: M.193, S.194, K.195 Ligands: AMP.6 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.195 Salt bridges: B:K.195

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.3: 12 residues within 4Å: Chain A: G.17, N.18, A.22, P.142, G.144, I.176, R.182, I.183, K.192, M.193 Ligands: TRP.1, PO4.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:P.142, A:G.144, A:I.183, A:I.183, A:K.192 pi-Cation interactions: A:K.192 AMP.6: 11 residues within 4Å: Chain B: G.17, N.18, G.21, G.144, D.146, Q.147, I.176, I.183, K.192 Ligands: TRP.4, PO4.5 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.144, B:D.146, B:Q.147, B:I.183, B:I.183, B:K.192 pi-Cation interactions: B:K.192

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Laowanapiban, P. et al., Independent saturation of three TrpRS subsites generates a partially assembled state similar to those observed in molecular simulations. Proc.Natl.Acad.Sci.Usa (2009)

Release Date

2009-02-03

Peptides

Tryptophanyl-tRNA synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
F

Tryptophanyl-tRNA synthetase

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