SMTL ID : 3a05.1

Crystal structure of tryptophanyl-tRNA synthetase from hyperthermophilic archaeon, Aeropyrum pernix K1 complex with tryptophan

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x TRP: TRYPTOPHAN(Non-covalent)

TRP.1: 9 residues within 4Å: Chain A: L.74, T.75, G.76, E.112, Q.151, Q.192, D.195, I.196 Ligands: CD.5 9 PLIP interactions: 9 interactions with chain A, Hydrophobic interactions: A:L.74, A:Q.192, A:I.196 Hydrogen bonds: A:Q.151, A:Q.192, A:D.195, A:D.195 Water bridges: A:M.78, A:Q.192 TRP.6: 9 residues within 4Å: Chain B: L.74, T.75, G.76, E.112, Q.151, Q.192, D.195, I.196 Ligands: CD.10 8 PLIP interactions: 8 interactions with chain B, Hydrophobic interactions: B:L.74, B:Q.192, B:I.196 Hydrogen bonds: B:Q.151, B:Q.192, B:D.195 Water bridges: B:M.78, B:Q.192

2 x SF4: IRON/SULFUR CLUSTER(Non-covalent)

SF4.2: 11 residues within 4Å: Chain A: T.284, G.285, G.286, C.303, V.305, Y.306, C.327, I.332, L.333, C.334, C.337 4 PLIP interactions: 4 interactions with chain A, Metal complexes: A:C.303, A:C.327, A:C.334, A:C.337 SF4.7: 11 residues within 4Å: Chain B: T.284, G.285, G.286, C.303, V.305, Y.306, C.327, I.332, L.333, C.334, C.337 4 PLIP interactions: 4 interactions with chain B, Metal complexes: B:C.303, B:C.327, B:C.334, B:C.337

6 x CD: CADMIUM ION(Non-covalent)

CD.3: 3 residues within 4Å: Chain A: W.342, E.343, E.346 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:E.343, A:E.343, A:E.346, A:E.346 CD.4: 2 residues within 4Å: Chain A: E.13, H.307 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.13, A:H.307, H2O.8, H2O.8, H2O.8 CD.5: 3 residues within 4Å: Chain A: E.112, Q.192 Ligands: TRP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.112, A:E.112, H2O.4, H2O.6 CD.8: 3 residues within 4Å: Chain B: W.342, E.343, E.346 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:E.343, B:E.343, B:E.346, B:E.346 CD.9: 2 residues within 4Å: Chain B: E.13, H.307 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.13, B:H.307, H2O.17, H2O.17, H2O.17 CD.10: 3 residues within 4Å: Chain B: E.112, Q.192 Ligands: TRP.6 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.112, B:E.112, H2O.13, H2O.15

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Tsuchiya, W. et al., Crystal structure of tryptophanyl-tRNA synthetase from hyperthermophilic archaeon, Aeropyrum pernix K1. To be Published

Release Date

2010-03-09

Peptides

Tryptophanyl-tRNA synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Tryptophanyl-tRNA synthetase

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