SMTL ID : 2ov4.1

Crystal structure of B. stearothermophilus tryptophanyl tRNA synthetase in complex with adenosine tetraphosphate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

2 x CS: CESIUM ION(Non-covalent)

CS.1: 4 residues within 4Å: Chain A: M.1, Q.30, Y.33, Q.74 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:Q.30, A:Y.33 CS.6: 4 residues within 4Å: Chain B: M.1, Q.30, Y.33, Q.74 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:Q.30, B:Y.33

2 x AQP: ADENOSINE-5'-TETRAPHOSPHATE(Non-covalent)

AQP.2: 22 residues within 4Å: Chain A: G.7, I.8, Q.9, S.11, G.17, N.18, G.21, A.22, K.111, V.143, G.144, D.146, Q.147, G.180, A.181, R.182, I.183, K.192, M.193, S.194, K.195, S.196 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:Q.9, A:Q.9, A:S.11, A:N.18, A:G.21, A:G.144, A:D.146, A:Q.147, A:I.183, A:I.183, A:M.193, A:K.195, A:S.196 Water bridges: A:S.6, A:N.18, A:N.18 Salt bridges: A:K.111, A:K.111, A:K.192, A:K.192, A:K.195, A:K.195, A:K.195, A:K.195 AQP.7: 22 residues within 4Å: Chain B: G.7, I.8, Q.9, S.11, G.17, N.18, G.21, A.22, K.111, V.143, G.144, D.146, Q.147, G.180, A.181, R.182, I.183, K.192, M.193, S.194, K.195, S.196 24 PLIP interactions: 24 interactions with chain B Hydrogen bonds: B:Q.9, B:Q.9, B:S.11, B:N.18, B:G.21, B:G.144, B:D.146, B:Q.147, B:I.183, B:I.183, B:M.193, B:K.195, B:S.196 Water bridges: B:S.6, B:N.18, B:N.18 Salt bridges: B:K.111, B:K.111, B:K.192, B:K.192, B:K.195, B:K.195, B:K.195, B:K.195

2 x ANL: ANILINE(Non-covalent)

ANL.3: 10 residues within 4Å: Chain A: F.5, S.6, G.7, V.40, H.43, M.129, D.132, I.133, V.141, V.143 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.5, A:F.5, A:D.132, A:I.133, A:V.141, A:V.143 Hydrogen bonds: A:H.43 ANL.8: 10 residues within 4Å: Chain B: F.5, S.6, G.7, V.40, H.43, M.129, D.132, I.133, V.141, V.143 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.5, B:F.5, B:D.132, B:I.133, B:V.141, B:V.143 Hydrogen bonds: B:D.132, B:D.132

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 5 residues within 4Å: Chain A: K.218, T.222, Y.265, G.266, K.269 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.218, A:K.218, A:T.222 GOL.5: 4 residues within 4Å: Chain A: R.60, Y.287, H.288, M.291 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.60, A:Y.287, A:H.288 GOL.9: 5 residues within 4Å: Chain B: K.218, T.222, Y.265, G.266, K.269 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.218, B:K.218 Water bridges: B:T.222 GOL.10: 4 residues within 4Å: Chain B: R.60, Y.287, H.288, M.291 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.60

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Retailleau, P. et al., Crystal Structure of Tryptophanyl-tRNA Synthetase Complexed with Adenosine-5' Tetraphosphate: Evidence for Distributed Use of Catalytic Binding Energy in Amino Acid Activation by Class I Aminoacyl-tRNA Synthetases. J.Mol.Biol. (2007)

Release Date

2007-03-06

Peptides

Tryptophanyl-tRNA synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Tryptophanyl-tRNA synthetase

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