SMTL ID : 2quj.1

Crystal structures of human tryptophanyl-tRNA synthetase in complex with TrpAMP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.42 Å

Oligo State

homo-dimer

Ligands

9 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 2 residues within 4Å: Chain A: H.473, H.474 Ligand excluded by PLIP CL.2: 4 residues within 4Å: Chain A: D.101, K.111, G.135, F.138 Ligand excluded by PLIP CL.3: 2 residues within 4Å: Chain A: K.204, D.205 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain A: I.384, R.388 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain A: D.113, K.114 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: H.257 Chain B: Y.201 Ligands: GOL.14 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain B: N.118, R.122 Ligand excluded by PLIP CL.11: 1 residues within 4Å: Chain B: D.205 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain B: D.113, K.114 Ligand excluded by PLIP

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

TYM.6: 21 residues within 4Å: Chain A: Y.159, T.160, G.161, R.162, G.163, G.172, I.175, P.176, Q.194, T.196, E.199, Q.284, I.307, C.309, A.310, Q.313, F.317, T.338, F.339, F.340, K.349 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:Y.159, A:I.307, A:Q.313, A:F.317, A:F.317 Hydrogen bonds: A:Y.159, A:Y.159, A:G.161, A:G.163, A:E.199, A:Q.284, A:A.310, A:F.340, A:F.340, A:K.349 Salt bridges: A:R.162, A:K.200

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 5 residues within 4Å: Chain A: Y.201, T.207, L.208, D.209 Chain B: K.253 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:D.209, A:D.209, B:K.253, B:K.253 GOL.8: 7 residues within 4Å: Chain A: G.380, R.381, D.382, T.383, I.384, L.426, T.427 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.381, A:T.427 Water bridges: A:G.428 GOL.14: 5 residues within 4Å: Chain A: K.253 Chain B: T.207, L.208, D.209 Ligands: CL.9 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:L.208, B:D.209, B:D.209, A:K.253 GOL.15: 8 residues within 4Å: Chain B: R.381, D.382, T.383, I.384, H.387, L.426, T.427, G.428 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.381, B:R.381, B:T.427, B:G.428

1 x TRP: TRYPTOPHAN(Non-covalent)

TRP.13: 12 residues within 4Å: Chain B: Y.159, T.160, G.161, R.162, G.163, Q.194, T.196, E.199, Q.284, C.309, Q.313, F.317 13 PLIP interactions: 12 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:Y.159, B:Q.313, B:F.317, B:F.317 Hydrogen bonds: B:Y.159, B:G.163, B:Q.284, B:Q.284 Water bridges: B:R.162, B:K.200, B:Q.313, W.13 Salt bridges: B:K.200

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shen, N. et al., Catalytic mechanism of the tryptophan activation reaction revealed by crystal structures of human tryptophanyl-tRNA synthetase in different enzymatic states. Nucleic Acids Res. (2008)

Release Date

2008-04-29

Peptides

Tryptophanyl-tRNA synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Tryptophanyl-tRNA synthetase

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