SMTL ID : 4rri.1

K116M mutant of N-terminal editing domain of threonyl-tRNA synthetase from Aeropyrum pernix with L-Thr3AA

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

2 x A3T: 3'-deoxy-3'-(L-threonylamino)adenosine(Non-covalent)

A3T.1: 17 residues within 4Å: Chain A: A.19, T.40, T.41, V.42, Y.73, P.74, Y.75, A.76, L.82, A.83, A.88, F.112, G.113, W.114, Y.115, M.116 Chain B: E.129 13 PLIP interactions: 12 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:Y.115 Hydrogen bonds: A:V.42, A:V.42, A:P.74, A:Y.75, A:A.76, A:A.83, A:G.113, A:W.114, A:W.114, A:M.116, A:M.116 Water bridges: B:E.129 A3T.3: 17 residues within 4Å: Chain A: E.129 Chain B: A.19, T.40, T.41, V.42, Y.73, P.74, Y.75, A.76, L.82, A.83, A.88, F.112, G.113, W.114, Y.115, M.116 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:Y.115 Hydrogen bonds: B:V.42, B:V.42, B:P.74, B:Y.75, B:A.76, B:A.83, B:G.113, B:W.114, B:W.114, B:M.116, B:M.116

2 x MG: MAGNESIUM ION(Non-functional Binders)

MG.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ahmad, S. et al., Specificity and catalysis hardwired at the RNA-protein interface in a translational proofreading enzyme. Nat Commun (2015)

Release Date

2015-07-15

Peptides

Probable threonine--tRNA ligase 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Probable threonine--tRNA ligase 2

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