SMTL ID : 3vqx.1 (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 AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.1: 14 residues within 4Å: Chain A: R.167, E.169, E.174, H.175, L.176, M.181, E.233, L.234, S.235, S.236, G.258, G.260, R.263, I.274 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:L.176, A:L.176, A:E.233, A:E.233, A:E.233, A:S.236, A:G.260 Salt bridges: A:R.167 pi-Stacking: A:F.179, A:F.179 AMP.3: 14 residues within 4Å: Chain B: R.167, E.169, E.174, H.175, L.176, F.179, M.181, E.233, L.234, S.235, S.236, G.258, G.260, R.263 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:L.176, B:L.176, B:E.233, B:E.233, B:S.236, B:S.236, B:G.260 Salt bridges: B:R.167 pi-Stacking: B:F.179, B:F.179

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

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

B
B

Pyrrolysine--tRNA ligase

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