SMTL ID : 5v0i.1

Crystal Structure of Tryptophanyl-tRNA Synthetase from Escherichia coli Complexed with AMP and Tryptophan

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 12 residues within 4Å: Chain A: G.22, N.23, G.26, A.27, G.150, P.183, A.187, R.188, V.189, K.198, M.199, K.201 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.23, A:V.189, A:K.198, A:M.199, A:M.199 Salt bridges: A:K.201 pi-Cation interactions: A:K.198 AMP.5: 11 residues within 4Å: Chain B: G.22, N.23, G.26, A.27, G.150, D.152, A.187, V.189, K.198, M.199, K.201 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.23, B:D.152, B:V.189, B:V.189, B:K.198, B:M.199 Salt bridges: B:K.198

2 x TRP: TRYPTOPHAN(Non-covalent)

TRP.2: 10 residues within 4Å: Chain A: F.10, G.12, Q.14, V.45, H.48, M.135, D.138, I.139, V.147, Q.153 13 PLIP interactions: 11 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:F.10, A:F.10, A:I.139, A:V.147 Hydrogen bonds: A:Q.14, A:D.138, A:D.138, A:Q.153, A:Q.153, W.2, W.2 Water bridges: A:Q.14 Salt bridges: A:K.201 TRP.6: 10 residues within 4Å: Chain B: F.10, G.12, Q.14, V.45, H.48, M.135, D.138, I.139, V.147, Q.153 11 PLIP interactions: 10 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:F.10, B:F.10, B:I.139, B:V.147 Hydrogen bonds: B:Q.14, B:D.138, B:D.138, B:Q.153, B:Q.153 pi-Stacking: B:H.48 Water bridges: W.6

4 x FMT: FORMIC ACID(Non-functional Binders)

FMT.3: 5 residues within 4Å: Chain A: H.39, I.41, T.81, K.315, H.319 1 PLIP interactions: 1 interactions with chain A Water bridges: A:H.319 FMT.4: 4 residues within 4Å: Chain A: Y.103, G.105, R.109 Chain B: E.122 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.109, A:R.109 FMT.7: 4 residues within 4Å: Chain B: H.39, I.41, T.81, H.319 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.81, B:H.319 FMT.8: 7 residues within 4Å: Chain A: C.100, Y.101, T.102, Y.103, R.166 Chain B: R.53, N.125 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.166, B:R.53

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maltseva, N. et al., Crystal Structure of Tryptophanyl-tRNA Synthetase from Escherichia coli Complexed with AMP and Tryptophan. To Be Published

Release Date

2017-03-22

Peptides

Tryptophan--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Tryptophan--tRNA ligase