SMTL ID : 1h4q.1

Prolyl-tRNA synthetase from Thermus thermophilus complexed with tRNApro(CGG), ATP and prolinol

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-dimer

Ligands

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 17 residues within 4Å: Chain A: R.142, E.144, F.150, L.151, R.152, T.153, F.156, W.158, Q.225, A.226, G.227, T.228, H.230, G.260, S.262, R.264 Ligands: PRI.3 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:R.142, A:T.153, A:T.153, A:Q.225, A:Q.225, A:T.228, A:T.228, A:S.262, A:S.262 Salt bridges: A:R.142, A:R.142, A:R.152, A:R.264 pi-Stacking: A:F.156, A:F.156 pi-Cation interactions: A:R.264, A:R.264 ATP.5: 17 residues within 4Å: Chain B: R.142, E.144, F.150, L.151, R.152, T.153, F.156, W.158, Q.225, A.226, G.227, T.228, H.230, G.260, S.262, R.264 Ligands: PRI.7 16 PLIP interactions: 16 interactions with chain B Hydrogen bonds: B:R.142, B:T.153, B:T.153, B:Q.225, B:Q.225, B:T.228, B:T.228, B:S.262, B:S.262 Salt bridges: B:R.142, B:R.142, B:R.152, B:R.264 pi-Stacking: B:F.156 pi-Cation interactions: B:R.264, B:R.264

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 5 residues within 4Å: Chain A: H.426, C.427, C.432, C.458, C.461 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.427, A:C.432, A:C.458, A:C.461 ZN.6: 4 residues within 4Å: Chain B: C.427, C.432, C.458, C.461 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.427, B:C.432, B:C.458, B:C.461

2 x PRI: PYRROLIDINE-2-CARBALDEHYDE(Non-covalent)

PRI.3: 11 residues within 4Å: Chain A: T.111, E.113, R.142, W.158, E.160, F.205, H.230, S.258, W.259, G.260 Ligands: ATP.1 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:W.158 Hydrogen bonds: A:E.113, A:R.142, A:S.258 PRI.7: 11 residues within 4Å: Chain B: T.111, E.113, R.142, W.158, E.160, F.205, H.230, S.258, W.259, G.260 Ligands: ATP.5 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.158 Hydrogen bonds: B:T.111, B:E.113, B:R.142, B:S.258

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

SO4.4: 4 residues within 4Å: Chain A: R.312, V.322, H.323, L.324 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.324 Salt bridges: A:R.312, A:H.323 SO4.8: 4 residues within 4Å: Chain B: R.312, V.322, H.323, L.324 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.324, B:L.324 Salt bridges: B:R.312, B:H.323

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yaremchuk, A. et al., A Succession of Substrate Induced Conformational Changes Ensures the Amino Acid Specificity of Thermus Thermophilus Prolyl-tRNA Synthetase: Comparison with Histidyl-tRNA Synthetase. J.Mol.Biol. (2001)

Release Date

2001-06-18

Peptides

PROLYL-TRNA SYNTHETASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

PROLYL-TRNA SYNTHETASE

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