SMTL ID : 8i4i.1

The asymmetric structure of homodimeric E. coli TrpRS bound with tryptophanyl adenylate and L-tryptophan

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

1 x TRP: TRYPTOPHAN(Non-covalent)

TRP.1: 10 residues within 4Å: Chain A: F.7, G.9, Q.11, V.42, H.45, M.132, D.135, I.136, V.144, Q.150 11 PLIP interactions: 9 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:F.7, A:F.7, A:V.42, A:I.136, A:V.144 Hydrogen bonds: A:Q.11, A:D.135, A:Q.150, A:Q.150, W.1, W.1

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 4 residues within 4Å: Chain A: N.20, M.196, S.197, K.198 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.20, A:M.196, A:K.198 Salt bridges: A:K.198 SO4.4: 5 residues within 4Å: Chain B: K.113, K.195, S.197, K.198, S.199 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:K.198, B:S.199 Water bridges: B:K.113, B:K.113, B:K.195, B:K.195, B:K.195, B:K.198, B:S.199 Salt bridges: B:K.113, B:K.195, B:K.198

1 x TYM: TRYPTOPHANYL-5'AMP(Non-covalent)

TYM.3: 27 residues within 4Å: Chain B: F.7, S.8, G.9, A.10, Q.11, G.19, N.20, G.23, A.24, V.42, H.45, Y.128, M.132, D.135, I.136, V.144, V.146, G.147, D.149, Q.150, G.183, A.184, R.185, V.186, K.195, M.196, K.198 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:F.7, B:F.7, B:V.42, B:I.136, B:V.144, B:V.146 Hydrogen bonds: B:Q.11, B:N.20, B:G.23, B:Y.128, B:Y.128, B:D.135, B:D.135, B:G.147, B:D.149, B:Q.150, B:V.186, B:V.186, B:K.195, B:M.196 Water bridges: B:P.145, B:E.148, B:D.149, B:Q.150 Salt bridges: B:K.198

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xiang, M. et al., An asymmetric structure of bacterial TrpRS supports the half-of-the-sites catalytic mechanism and facilitates antimicrobial screening. Nucleic Acids Res. (2023)

Release Date

2023-04-12

Peptides

Tryptophan--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Tryptophan--tRNA ligase

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