SMTL ID : 3vqx.2 (1 other biounit)

Crystal structure of the catalytic domain of pyrrolysyl-tRNA synthetase in triclinic crystal form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

homo-dimer

Ligands

2 x BLK: [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] (2S)-2-azanyl-6-[(2-methylpropan-2-yl)oxycarbonylamino]hexanoate(Non-covalent)

BLK.1: 20 residues within 4Å: Chain A: A.139, Y.143, R.167, H.175, L.176, F.179, M.181, N.183, C.185, E.233, L.234, S.235, S.236, V.238, W.254, G.258, F.259, G.260, R.263, I.274 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:Y.143, A:W.254 Hydrogen bonds: A:R.167, A:L.176, A:L.176, A:N.183, A:E.233, A:S.236, A:S.236, A:G.260, A:R.263 Salt bridges: A:R.167 pi-Stacking: A:F.179, A:F.179 pi-Cation interactions: A:R.263 BLK.3: 22 residues within 4Å: Chain B: A.139, L.142, Y.143, R.167, E.169, E.174, H.175, L.176, F.179, M.181, N.183, C.185, E.233, L.234, S.235, S.236, V.238, W.254, G.258, F.259, G.260, R.263 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:L.142, B:Y.143, B:V.238, B:W.254, B:W.254 Hydrogen bonds: B:E.169, B:L.176, B:L.176, B:N.183, B:N.183, B:E.233, B:E.233, B:E.233, B:S.236, B:G.260, B:R.263 Water bridges: B:R.167, B:R.167 Salt bridges: B:R.167 pi-Stacking: B:F.179, B:F.179 pi-Cation interactions: B:H.175

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 4 residues within 4Å: Chain A: R.147, K.148, R.151 Chain B: N.290 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Salt bridges: A:R.147, A:K.148, A:R.151 Hydrogen bonds: B:N.290 PO4.4: 4 residues within 4Å: Chain A: N.290 Chain B: R.147, K.148, R.151 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:N.290 Salt bridges: B:R.147, B:K.148, B:R.151

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yanagisawa, T. et al., A novel crystal form of pyrrolysyl-tRNA synthetase reveals the pre- and post-aminoacyl-tRNA synthesis conformational states of the adenylate and aminoacyl moieties and an asparagine residue in the catalytic site. Acta Crystallogr.,Sect.D (2013)

Release Date

2013-01-02

Peptides

Pyrrolysine--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

Pyrrolysine--tRNA ligase

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