SMTL ID : 4k87.1

Crystal structure of human prolyl-tRNA synthetase (substrate bound form)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.471, C.476, C.518, C.520 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.471, A:C.476, A:C.518, A:C.520 ZN.4: 4 residues within 4Å: Chain B: C.471, C.476, C.518, C.520 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.471, B:C.476, B:C.518, B:C.520

2 x ADN: ADENOSINE(Non-covalent)

ADN.2: 13 residues within 4Å: Chain A: R.175, F.184, L.185, R.186, T.187, F.190, Q.260, G.262, T.263, G.297, T.299, R.301 Ligands: PRO.3 12 PLIP interactions: 11 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:R.175, A:R.175, A:T.187, A:T.187, A:Q.260, A:T.263, A:T.263, A:R.301, P.3 pi-Stacking: A:F.190 pi-Cation interactions: A:R.301, A:R.301 ADN.5: 13 residues within 4Å: Chain B: R.175, F.184, L.185, R.186, T.187, F.190, Q.260, G.262, T.263, G.297, T.299, R.301 Ligands: PRO.6 13 PLIP interactions: 12 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: B:R.175, B:R.175, B:T.187, B:T.187, B:Q.260, B:T.263, B:T.263, B:T.299, B:R.301, P.6 pi-Stacking: B:F.190 pi-Cation interactions: B:R.301, B:R.301

2 x PRO: PROLINE(Non-covalent)

PRO.3: 13 residues within 4Å: Chain A: T.144, E.146, R.175, W.192, E.194, H.196, F.239, T.263, H.265, S.295, W.296, G.297 Ligands: ADN.2 11 PLIP interactions: 10 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:W.192, A:W.192, A:E.194 Hydrogen bonds: A:T.144, A:T.144, A:T.263, A:T.263, A:S.295, P.3 Salt bridges: A:R.175, A:H.265 PRO.6: 13 residues within 4Å: Chain B: T.144, E.146, R.175, W.192, E.194, H.196, F.239, T.263, H.265, S.295, W.296, G.297 Ligands: ADN.5 9 PLIP interactions: 8 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:W.192, B:W.192, B:E.194 Hydrogen bonds: B:T.144, B:T.263, B:S.295, P.6 Salt bridges: B:R.175, B:H.265

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Son, J. et al., Conformational changes in human prolyl-tRNA synthetase upon binding of the substrates proline and ATP and the inhibitor halofuginone. Acta Crystallogr.,Sect.D (2013)

Release Date

2013-10-09

Peptides

Proline--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Proline--tRNA ligase

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