SMTL ID : 5n5u.1

Structure of p-boronophenylalanyl tRNA synthetase in complex with p-boronophenylalanine and adenosine monophosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 17 residues within 4Å: Chain A: G.34, F.35, E.36, H.42, G.44, H.45, Q.48, G.169, G.170, E.172, Q.173, P.194, V.195, L.196, K.204, M.205 Ligands: 7N8.2 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:E.36, A:Q.48, A:G.170, A:E.172, A:L.196, A:M.205, A:M.205 Water bridges: A:H.45 Salt bridges: A:H.45 AMP.6: 17 residues within 4Å: Chain B: G.34, F.35, E.36, H.42, G.44, H.45, Q.48, G.169, G.170, E.172, Q.173, P.194, V.195, L.196, K.204, M.205 Ligands: 7N8.7 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:E.36, B:Q.48, B:G.170, B:E.172, B:L.196, B:M.205, B:M.205 Water bridges: B:H.45 Salt bridges: B:H.45

2 x 7N8: 4-Borono-L-phenylalanine(Non-covalent)

7N8.2: 12 residues within 4Å: Chain A: G.34, E.36, A.65, A.67, M.70, I.137, Y.151, Q.155, S.158, E.162, Q.173 Ligands: AMP.1 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:A.67, A:Q.155 Hydrogen bonds: A:S.32, A:E.36, A:E.36, A:Y.151, A:Q.155, A:Q.155, A:S.158, A:Q.173, A:Q.173 Water bridges: A:S.32, A:Q.109, A:E.162 7N8.7: 12 residues within 4Å: Chain B: G.34, E.36, A.65, A.67, M.70, I.137, Y.151, Q.155, S.158, E.162, Q.173 Ligands: AMP.6 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:A.67, B:Q.155 Hydrogen bonds: B:S.32, B:E.36, B:Y.151, B:Q.155, B:Q.155, B:S.158, B:Q.173, B:Q.173 Water bridges: B:S.32, B:Q.109, B:E.162

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 5 residues within 4Å: Chain A: R.257, E.281, L.282, H.283, R.286 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: V.235, V.236, E.237 Ligand excluded by PLIP CL.5: 4 residues within 4Å: Chain A: L.127, R.131 Chain B: R.131 Ligands: CL.10 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain B: R.257, E.281, L.282, H.283, R.286 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain B: V.235, V.236, E.237 Ligand excluded by PLIP CL.10: 4 residues within 4Å: Chain A: R.131 Chain B: L.127, R.131 Ligands: CL.5 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schiefner, A. et al., Structural Basis for the Specific Cotranslational Incorporation of p-Boronophenylalanine into Biosynthetic Proteins. Biochemistry (2018)

Release Date

2018-02-14

Peptides

Tyrosine--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Tyrosine--tRNA ligase

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