SMTL ID : 4cs2.1

Catalytic domain of Pyrrolysyl-tRNA synthetase mutant Y306A, Y384F in its apo form

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

homo-dimer

Ligands

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.1: 7 residues within 4Å: Chain A: A.116, A.120, L.123, N.160, W.231, G.233, A.234 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.222, A:D.222 PEG.6: 7 residues within 4Å: Chain B: A.116, A.120, L.123, N.160, W.231, G.233, A.234 1 PLIP interactions: 1 interactions with chain B Water bridges: B:D.222

8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 6 residues within 4Å: Chain A: Y.56, L.60, E.63, L.242, K.245, H.246 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.63, A:K.245, A:H.246 EDO.3: 8 residues within 4Å: Chain A: N.55, R.253, A.254, A.255, Y.260, Y.261, N.262, G.263 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.55, A:N.55, A:R.253, A:N.262, A:G.263 EDO.4: 4 residues within 4Å: Chain A: F.103, E.154 Chain B: D.106, F.109 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.106 EDO.5: 6 residues within 4Å: Chain A: G.165, S.166, G.167, C.168, T.169, P.230 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.165, A:C.168 Water bridges: A:G.167 EDO.7: 6 residues within 4Å: Chain B: Y.56, L.60, E.63, L.242, K.245, H.246 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.63, B:K.245, B:H.246 EDO.8: 8 residues within 4Å: Chain B: N.55, R.253, A.254, A.255, Y.260, Y.261, N.262, G.263 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.55, B:N.55, B:R.253, B:N.262, B:G.263 EDO.9: 4 residues within 4Å: Chain A: D.106, F.109 Chain B: F.103, E.154 No protein-ligand interaction detected (PLIP) EDO.10: 6 residues within 4Å: Chain B: G.165, S.166, G.167, C.168, T.169, P.230 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:G.165, B:C.168 Water bridges: B:G.167

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schmidt, M.J. et al., Structural Basis of Furan-Amino Acid Recognition by a Polyspecific Aminoacyl-tRNA-Synthetase and its Genetic Encoding in Human Cells. Chembiochem (2014)

Release Date

2014-04-30

Peptides

PYRROLYSINE--TRNA LIGASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

PYRROLYSINE--TRNA LIGASE

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