SMTL ID : 1i6k.1

1.7 HIGH RESOLUTION EXPERIMENTAL PHASES FOR TRYPTOPHANYL-TRNA SYNTHETASE COMPLEXED WITH TRYPTOPHANYL-5'AMP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.72 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: Y.98, R.160, K.163, R.164 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.98, A:R.164 Water bridges: A:K.163, A:K.163 Salt bridges: A:R.160, A:K.163 SO4.2: 3 residues within 4Å: Chain A: T.222, Y.265, K.269 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.222, A:T.222 Water bridges: A:G.266 Salt bridges: A:K.269 SO4.3: 3 residues within 4Å: Chain A: R.55 Chain B: Q.320 Ligands: GOL.13 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.320 Salt bridges: A:R.55 SO4.4: 3 residues within 4Å: Chain A: G.264, Y.265, G.266 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.266 Water bridges: A:G.264, A:Y.265, A:Y.265, A:V.267 SO4.5: 4 residues within 4Å: Chain A: R.182, M.184, T.190, K.232 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.182, A:K.232 SO4.6: 6 residues within 4Å: Chain A: K.178, G.180, A.181, R.182, Y.230, N.243 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.180, A:A.181, A:R.182, A:R.182, A:Y.230, A:N.243 Water bridges: A:P.177, A:K.178 SO4.7: 3 residues within 4Å: Chain A: R.60, Y.287, M.291 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.287, A:Y.287 Salt bridges: A:R.60 SO4.14: 4 residues within 4Å: Chain B: Y.98, R.160, K.163, R.164 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:R.164 Water bridges: B:K.163, B:K.163 Salt bridges: B:R.160, B:K.163 SO4.15: 3 residues within 4Å: Chain B: T.222, Y.265, K.269 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.222 Water bridges: B:G.266 Salt bridges: B:K.269 SO4.16: 3 residues within 4Å: Chain A: Q.320 Chain B: R.55 Ligands: GOL.26 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.320 Salt bridges: B:R.55 SO4.17: 3 residues within 4Å: Chain B: G.264, Y.265, G.266 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.266 Water bridges: B:G.264, B:Y.265, B:Y.265, B:V.267 SO4.18: 4 residues within 4Å: Chain B: R.182, M.184, T.190, K.232 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.182, B:K.232 SO4.19: 6 residues within 4Å: Chain B: K.178, G.180, A.181, R.182, Y.230, N.243 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.180, B:A.181, B:R.182, B:R.182, B:N.243 Water bridges: B:P.177, B:K.178 SO4.20: 3 residues within 4Å: Chain B: R.60, Y.287, M.291 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.287 Salt bridges: B:R.60

2 x NH4: AMMONIUM ION(Non-functional Binders)

NH4.8: 5 residues within 4Å: Chain A: Q.30, H.31, Y.33, Q.74 Ligands: GOL.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.33 NH4.21: 5 residues within 4Å: Chain B: Q.30, H.31, Y.33, Q.74 Ligands: GOL.23 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.30

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

TYM.9: 26 residues within 4Å: Chain A: F.5, S.6, G.7, I.8, Q.9, G.17, N.18, G.21, A.22, V.40, H.43, Y.125, M.129, D.132, I.133, V.141, V.143, G.144, D.146, Q.147, G.180, A.181, R.182, I.183, K.192, M.193 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:F.5, A:F.5, A:V.40, A:I.133, A:V.141, A:V.143 Hydrogen bonds: A:Q.9, A:N.18, A:G.21, A:Y.125, A:G.144, A:D.146, A:I.183, A:I.183, A:K.192 Water bridges: A:K.111, A:P.142, A:E.145, A:E.145, A:Q.147, A:Q.147, A:Q.147, A:K.195 Salt bridges: A:K.195 TYM.22: 26 residues within 4Å: Chain B: F.5, S.6, G.7, I.8, Q.9, G.17, N.18, G.21, A.22, V.40, H.43, Y.125, M.129, D.132, I.133, V.141, V.143, G.144, D.146, Q.147, G.180, A.181, R.182, I.183, K.192, M.193 28 PLIP interactions: 28 interactions with chain B Hydrophobic interactions: B:F.5, B:F.5, B:V.40, B:I.133, B:V.141, B:V.143 Hydrogen bonds: B:Q.9, B:N.18, B:G.21, B:H.43, B:Y.125, B:Y.125, B:D.132, B:G.144, B:D.146, B:I.183, B:I.183, B:K.192 Water bridges: B:T.15, B:P.142, B:E.145, B:D.146, B:Q.147, B:Q.147, B:H.150, B:H.150, B:K.195 Salt bridges: B:K.195

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 10 residues within 4Å: Chain A: Y.33, N.34, C.35, Y.36, T.73, Q.74, A.75, T.76, K.306 Ligands: NH4.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:C.35, A:T.73, A:Q.74, A:K.306 GOL.11: 10 residues within 4Å: Chain A: S.11, G.12, V.13, I.14, N.57, R.60, L.64, T.205, L.206, L.207 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.14, A:L.206 Water bridges: A:S.11, A:L.61 GOL.12: 2 residues within 4Å: Chain A: K.306, R.309 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.309, A:R.309 Water bridges: A:K.306 GOL.13: 5 residues within 4Å: Chain A: H.52, R.55, Q.56, R.59 Ligands: SO4.3 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.52, A:R.55, A:Q.56 Water bridges: A:H.52, A:H.52 GOL.23: 10 residues within 4Å: Chain B: Y.33, N.34, C.35, Y.36, T.73, Q.74, A.75, T.76, K.306 Ligands: NH4.21 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:C.35, B:T.73, B:Q.74, B:T.76, B:K.306 GOL.24: 10 residues within 4Å: Chain B: S.11, G.12, V.13, I.14, N.57, R.60, L.64, T.205, L.206, L.207 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:I.14, B:L.206 Water bridges: B:S.11, B:L.61 GOL.25: 2 residues within 4Å: Chain B: K.306, R.309 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.309, B:R.309 Water bridges: B:K.306 GOL.26: 5 residues within 4Å: Chain B: H.52, R.55, Q.56, R.59 Ligands: SO4.16 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:H.52, B:R.55, B:Q.56

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Retailleau, P. et al., High-resolution experimental phases for tryptophanyl-tRNA synthetase (TrpRS) complexed with tryptophanyl-5'AMP. Acta Crystallogr.,Sect.D (2001)

Release Date

2001-11-07

Peptides

TRYPTOPHANYL-TRNA SYNTHETASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

TRYPTOPHANYL-TRNA SYNTHETASE

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