SMTL ID : 6ab0.1

Crystal structure of Methanosarcina mazei PylRS(Y306A/Y384F) complexed with pAmPyLys

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.44 Å

Oligo State

homo-dimer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: R.150 Ligands: ATP.4 No protein-ligand interaction detected (PLIP) MG.2: 4 residues within 4Å: Chain A: E.216, S.219 Ligands: MG.3, ATP.4 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.216, A:S.219, H2O.3, H2O.6 MG.3: 3 residues within 4Å: Chain A: E.216 Ligands: MG.2, ATP.4 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.216, H2O.3, H2O.7, H2O.8 MG.10: 2 residues within 4Å: Chain B: R.150 Ligands: ATP.13 No protein-ligand interaction detected (PLIP) MG.11: 4 residues within 4Å: Chain B: E.216, S.219 Ligands: MG.12, ATP.13 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.216, B:S.219, H2O.14, H2O.18 MG.12: 3 residues within 4Å: Chain B: E.216 Ligands: MG.11, ATP.13 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.216, H2O.14, H2O.19, H2O.19

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.4: 18 residues within 4Å: Chain A: R.150, E.152, E.157, H.158, L.159, F.162, M.164, E.216, L.217, S.218, S.219, G.241, G.243, R.246 Ligands: MG.1, MG.2, MG.3, 9UF.5 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:E.152, A:L.159, A:E.216, A:E.216, A:S.219, A:G.243, A:R.246 Water bridges: A:R.150, A:R.150, A:R.150, A:R.150, A:H.158, A:H.158, A:E.216, A:E.216, A:R.246 Salt bridges: A:R.150, A:R.150, A:H.158, A:R.246 pi-Stacking: A:F.162, A:F.162 pi-Cation interactions: A:R.246, A:R.246 ATP.13: 18 residues within 4Å: Chain B: R.150, E.152, E.157, H.158, L.159, F.162, M.164, E.216, L.217, S.218, S.219, G.241, G.243, R.246 Ligands: MG.10, MG.11, MG.12, 9UF.14 24 PLIP interactions: 24 interactions with chain B Hydrogen bonds: B:E.152, B:E.152, B:L.159, B:E.216, B:E.216, B:E.216, B:S.219, B:G.243, B:R.246 Water bridges: B:R.150, B:R.150, B:R.150, B:R.150, B:H.158, B:H.158, B:R.246 Salt bridges: B:R.150, B:R.150, B:H.158, B:R.246 pi-Stacking: B:F.162, B:F.162 pi-Cation interactions: B:R.246, B:R.246

2 x 9UF: N6-{[(6-aminopyridin-3-yl)methoxy]carbonyl}-L-lysine(Non-covalent)

9UF.5: 18 residues within 4Å: Chain A: M.120, A.122, A.126, L.129, R.150, M.164, N.166, F.167, C.168, F.204, S.219, V.221, D.228, W.237, G.239, A.240, G.241 Ligands: ATP.4 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.129, A:F.204, A:V.221 Hydrogen bonds: A:R.150, A:N.166, A:D.228, A:D.228 Water bridges: A:N.166 Salt bridges: A:R.150 pi-Stacking: A:W.237 9UF.14: 18 residues within 4Å: Chain B: M.120, A.122, A.126, L.129, R.150, M.164, N.166, F.167, C.168, F.204, S.219, V.221, D.228, W.237, G.239, A.240, G.241 Ligands: ATP.13 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.129, B:F.204, B:V.221 Hydrogen bonds: B:R.150, B:N.166, B:D.228 Water bridges: B:N.166 Salt bridges: B:R.150 pi-Stacking: B:W.237

6 x K: POTASSIUM ION(Non-covalent)

K.6: 4 residues within 4Å: Chain A: L.22, N.23, P.24, D.26 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:N.23, H2O.1, H2O.8, H2O.10 K.7: 2 residues within 4Å: Chain A: E.161, R.262 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.161, A:R.262, H2O.8 K.8: 5 residues within 4Å: Chain A: G.155, H.158, N.256, I.257, K.258 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:G.155, A:H.158 K.15: 4 residues within 4Å: Chain B: L.22, N.23, P.24, D.26 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:N.23, H2O.12, H2O.19, H2O.22 K.16: 2 residues within 4Å: Chain B: E.161, R.262 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.161, B:R.262, H2O.20 K.17: 5 residues within 4Å: Chain B: G.155, H.158, N.256, I.257, K.258 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:G.155, B:H.158

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

PO4.9: 3 residues within 4Å: Chain A: E.60 Chain B: T.71, R.72 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain A Water bridges: B:R.72, B:R.72, A:R.68 Salt bridges: B:R.72, A:R.68 PO4.18: 3 residues within 4Å: Chain A: T.71, R.72 Chain B: E.60 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain B Water bridges: A:R.72, A:R.72, B:R.68 Salt bridges: A:R.72, B:R.68

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yanagisawa, T. et al., Structural Basis for Genetic-Code Expansion with Bulky Lysine Derivatives by an Engineered Pyrrolysyl-tRNA Synthetase. Cell Chem Biol (2019)

Release Date

2019-04-17

Peptides

Pyrrolysine--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Pyrrolysine--tRNA ligase

Related Entries With Identical Sequence