SMTL ID : 2amc.1

Crystal structure of Phenylalanyl-tRNA synthetase complexed with L-tyrosine

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

hetero-2-2-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: E.178 Chain B: D.452, E.461 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Metal complexes: A:E.178, B:E.461 MG.5: 3 residues within 4Å: Chain C: E.178 Chain D: D.452, E.461 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Metal complexes: D:E.461, C:E.178

4 x TYR: TYROSINE(Non-covalent)

TYR.2: 15 residues within 4Å: Chain A: W.65, T.93, H.94, S.96, R.120, Q.134, E.136, F.174, F.176, V.177, G.198, A.199, A.230, F.231, G.232 12 PLIP interactions: 10 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:F.174 Hydrogen bonds: A:H.94, A:S.96, A:Q.134, Y.2, Y.2 Water bridges: A:S.96, A:Q.99 Salt bridges: A:H.94, A:R.120 pi-Stacking: A:F.174, A:F.176 TYR.4: 12 residues within 4Å: Chain B: P.259, M.260, H.261, L.286, G.315, V.316, M.317, G.318, E.334, F.338, A.356, F.360 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:H.261, B:A.356 Hydrogen bonds: B:M.260, B:G.315, B:V.316, B:G.318 Water bridges: B:A.262 Salt bridges: B:H.261 TYR.6: 15 residues within 4Å: Chain C: W.65, T.93, H.94, S.96, R.120, Q.134, E.136, F.174, F.176, V.177, G.198, A.199, A.230, F.231, G.232 13 PLIP interactions: 11 interactions with chain C, 2 Ligand-Ligand interactions Hydrophobic interactions: C:F.174 Hydrogen bonds: C:H.94, C:S.96, C:S.96, C:Q.134, Y.6, Y.6 Water bridges: C:S.96, C:Q.99 Salt bridges: C:H.94, C:R.120 pi-Stacking: C:F.174, C:F.176 TYR.8: 12 residues within 4Å: Chain D: P.259, M.260, H.261, L.286, G.315, V.316, M.317, G.318, E.334, F.338, A.356, F.360 10 PLIP interactions: 10 interactions with chain D, Hydrophobic interactions: D:H.261, D:A.356 Hydrogen bonds: D:M.260, D:G.315, D:V.316, D:G.318 Water bridges: D:H.261, D:A.262, D:T.354 Salt bridges: D:H.261

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

SO4.3: 3 residues within 4Å: Chain B: R.407, Y.410, R.413 4 PLIP interactions: 4 interactions with chain B Water bridges: B:Y.410, B:Y.410 Salt bridges: B:R.407, B:R.413 SO4.7: 3 residues within 4Å: Chain D: R.407, Y.410, R.413 2 PLIP interactions: 2 interactions with chain D Salt bridges: D:R.407, D:R.413

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kotik-Kogan, O. et al., Structural Basis for Discrimination of L-Phenylalanine from L-Tyrosine by Phenylalanyl-tRNA Synthetase. Structure (2005)

Release Date

2005-12-20

Peptides

Phenylalanyl-tRNA synthetase alpha chain: AC
Phenylalanyl-tRNA synthetase beta chain: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

Phenylalanyl-tRNA synthetase alpha chain

Phenylalanyl-tRNA synthetase beta chain

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