SMTL ID : 3qtc.1

Crystal structure of the catalytic domain of MmOmeRS, an O-methyl tyrosyl-tRNA synthetase evolved from Methanosarcina mazei PylRS, complexed with O-methyl tyrosine and AMP-PNP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: R.166, H.174 Ligands: ANP.9 No protein-ligand interaction detected (PLIP) MG.2: 3 residues within 4Å: Chain A: E.232, S.235 Ligands: ANP.9 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.232, H2O.7, H2O.8 MG.10: 3 residues within 4Å: Chain B: R.166, H.174 Ligands: ANP.18 No protein-ligand interaction detected (PLIP) MG.11: 3 residues within 4Å: Chain B: E.232, S.235 Ligands: ANP.18 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.232, H2O.16, H2O.17

2 x 0A1: O-methyl-L-tyrosine(Non-covalent)

0A1.3: 13 residues within 4Å: Chain A: M.136, T.138, M.180, V.182, W.184, S.235, L.237, W.253, G.255, A.256, G.257 Ligands: EDO.4, ANP.9 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.182, A:V.182, A:L.237 Water bridges: A:T.138 0A1.12: 13 residues within 4Å: Chain B: M.136, T.138, M.180, V.182, W.184, S.235, L.237, W.253, G.255, A.256, G.257 Ligands: EDO.13, ANP.18 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.182, B:V.182, B:L.237 Water bridges: B:T.138

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

EDO.4: 7 residues within 4Å: Chain A: T.138, Y.142, L.237, I.241, L.243, W.253 Ligands: 0A1.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.142 EDO.5: 5 residues within 4Å: Chain A: L.231, K.265, V.266, D.269, F.270 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.265, A:D.269, A:F.270 EDO.6: 7 residues within 4Å: Chain A: Y.78, K.81, L.82, E.85, L.264, K.267, H.268 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.85, A:K.267, A:H.268 Water bridges: A:K.81, A:K.81 EDO.7: 9 residues within 4Å: Chain A: N.77, Y.78, R.275, A.276, A.277, Y.282, Y.283, N.284, G.285 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.77, A:N.77, A:R.275, A:N.284, A:G.285 EDO.8: 1 residues within 4Å: Chain A: E.193 No protein-ligand interaction detected (PLIP) EDO.13: 7 residues within 4Å: Chain B: T.138, Y.142, L.237, I.241, L.243, W.253 Ligands: 0A1.12 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.142 EDO.14: 5 residues within 4Å: Chain B: L.231, K.265, V.266, D.269, F.270 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.265, B:D.269, B:F.270 EDO.15: 7 residues within 4Å: Chain B: Y.78, K.81, L.82, E.85, L.264, K.267, H.268 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.85, B:K.267, B:H.268 Water bridges: B:K.81, B:K.81 EDO.16: 9 residues within 4Å: Chain B: N.77, Y.78, R.275, A.276, A.277, Y.282, Y.283, N.284, G.285 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.77, B:N.77, B:R.275, B:N.284, B:G.285 EDO.17: 1 residues within 4Å: Chain B: E.193 No protein-ligand interaction detected (PLIP)

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.9: 16 residues within 4Å: Chain A: R.166, E.168, H.174, L.175, F.178, M.180, E.232, L.233, S.234, S.235, G.257, G.259, R.262 Ligands: MG.1, MG.2, 0A1.3 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:R.166, A:E.168, A:H.174, A:L.175, A:E.232, A:E.232, A:E.232, A:S.235, A:G.259, A:R.262, A:R.262 Water bridges: A:H.174, A:S.235 Salt bridges: A:R.166 pi-Stacking: A:F.178, A:F.178 pi-Cation interactions: A:R.262, A:R.262 ANP.18: 16 residues within 4Å: Chain B: R.166, E.168, H.174, L.175, F.178, M.180, E.232, L.233, S.234, S.235, G.257, G.259, R.262 Ligands: MG.10, MG.11, 0A1.12 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:R.166, B:E.168, B:H.174, B:L.175, B:E.232, B:E.232, B:E.232, B:S.235, B:G.259, B:R.262, B:R.262 Water bridges: B:H.174, B:S.235, B:S.235 Salt bridges: B:R.166 pi-Stacking: B:F.178, B:F.178 pi-Cation interactions: B:R.262, B:R.262

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Takimoto, J.K. et al., Stereochemical Basis for Engineered Pyrrolysyl-tRNA Synthetase and the Efficient in Vivo Incorporation of Structurally Divergent Non-native Amino Acids. Acs Chem.Biol. (2011)

Release Date

2011-05-25

Peptides

Pyrrolysyl-tRNA synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Pyrrolysyl-tRNA synthetase