SMTL ID : 4h3s.1

The Structure of Glutaminyl-tRNA Synthetase from Saccharomyces Cerevisiae

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.15 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain A: Y.344, C.346, H.347, C.348, C.372, H.374, R.402 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.346, A:C.348, A:C.372, A:H.374

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 11 residues within 4Å: Chain A: F.256, P.257, P.258, E.259, H.268, A.271, C.458, T.459, Y.486 Ligands: GOL.3, BR.10 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.268 Water bridges: A:R.255, A:G.267, A:N.275, A:Y.486 GOL.3: 7 residues within 4Å: Chain A: H.265, G.267, H.268, T.459, R.488, L.489 Ligands: GOL.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.265, A:L.489 Water bridges: A:G.267, A:T.459, A:R.488, A:L.489 GOL.4: 8 residues within 4Å: Chain A: L.574, V.705, Y.734, R.780, V.781, G.782, F.784, R.799 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.799 GOL.5: 10 residues within 4Å: Chain A: S.324, D.325, Y.326, F.327, D.328, E.329, T.430, K.433, W.434 Ligands: GOL.9 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.325, A:D.325, A:D.328, A:K.433, A:W.434 GOL.6: 8 residues within 4Å: Chain A: R.255, H.444, C.458, F.462, S.465, R.466, Y.469, Q.483 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.444, A:S.465, A:Q.483 Water bridges: A:R.255, A:R.255, A:H.444 GOL.7: 11 residues within 4Å: Chain A: P.260, D.292, N.294, P.295, E.296, F.303, Y.322, S.324, H.427, P.428, R.429 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.292, A:D.292, A:N.294, A:E.296 GOL.8: 3 residues within 4Å: Chain A: N.583, L.584, S.585 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.585 Water bridges: A:N.583, A:N.583, A:S.585, A:N.670 GOL.9: 6 residues within 4Å: Chain A: D.328, R.429, T.430, G.431, K.433 Ligands: GOL.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.328, A:T.430, A:K.433

1 x BR: BROMIDE ION(Non-covalent)

BR.10: 4 residues within 4Å: Chain A: C.458, T.459, F.462 Ligands: GOL.2 Ligand excluded by PLIP

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

CL.11: 5 residues within 4Å: Chain A: R.517, P.728, E.729, S.730, E.731 Ligand excluded by PLIP

4 x ACT: ACETATE ION(Non-functional Binders)

ACT.12: 8 residues within 4Å: Chain A: F.743, V.747, K.771, L.786, S.790, T.791, T.792, V.795 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.786 Hydrogen bonds: A:S.790 Salt bridges: A:K.771 ACT.13: 7 residues within 4Å: Chain A: H.228, K.229, V.230, V.252, Y.278, H.282, H.455 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.230, A:Y.278 Water bridges: A:H.282 Salt bridges: A:H.282, A:H.455 ACT.14: 10 residues within 4Å: Chain A: G.262, Y.263, L.264, H.265, L.496, S.497, K.498, I.501, W.513, T.520 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.501, A:T.520 Hydrogen bonds: A:Y.263 ACT.15: 5 residues within 4Å: Chain A: L.641, I.642, K.643, V.644, Y.684 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.684 Hydrogen bonds: A:K.643 Salt bridges: A:K.643

1 x DTT: 2,3-DIHYDROXY-1,4-DITHIOBUTANE(Non-covalent)

DTT.16: 6 residues within 4Å: Chain A: D.328, R.390, D.391, K.433, W.434, R.435 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.433, A:K.433

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Grant, T.D. et al., The Structure of Yeast Glutaminyl-tRNA Synthetase and Modeling of Its Interaction with tRNA. J.Mol.Biol. (2013)

Release Date

2013-04-24

Peptides

Glutamine-tRNA ligase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Glutamine-tRNA ligase