SMTL ID : 6aan.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.51 Å

Oligo State

homo-dimer

Ligands

6 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 2 residues within 4Å: Chain A: H.158 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 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.216, A:S.219 MG.3: 3 residues within 4Å: Chain A: E.216 Ligands: MG.2, ATP.4 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.216, H2O.2 MG.9: 2 residues within 4Å: Chain B: H.158 Ligands: ATP.12 No protein-ligand interaction detected (PLIP) MG.10: 4 residues within 4Å: Chain B: E.216, S.219 Ligands: MG.11, ATP.12 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:E.216, B:S.219 MG.11: 3 residues within 4Å: Chain B: E.216 Ligands: MG.10, ATP.12 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.216, H2O.11

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, 9TX.5 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:E.152, A:L.159, A:E.216, A:S.219, A:G.243, A:R.246 Water bridges: A:R.150, A:R.150, A:R.150, A:E.157, A:E.216 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.12: 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.9, MG.10, MG.11, 9TX.13 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:E.152, B:E.152, B:L.159, B:E.216, B:S.219, B:G.243, B:R.246 Water bridges: B:R.150, B:R.150, B:R.150, B:E.157, B:E.216 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 9TX: N6-{[(3-ethynylphenyl)methoxy]carbonyl}-L-lysine(Non-covalent)

9TX.5: 24 residues within 4Å: Chain A: M.96, M.120, A.122, L.125, A.126, L.129, M.164, N.166, F.167, C.168, C.201, F.204, S.219, A.220, V.221, L.227, D.228, W.231, I.233, W.237, G.239, A.240, G.241 Ligands: ATP.4 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:A.126, A:L.129, A:L.227, A:I.233 Hydrogen bonds: A:N.166 Water bridges: A:A.122, A:N.166 pi-Stacking: A:W.237 9TX.13: 24 residues within 4Å: Chain B: M.96, M.120, A.122, L.125, A.126, L.129, M.164, N.166, F.167, C.168, C.201, F.204, S.219, A.220, V.221, L.227, D.228, W.231, I.233, W.237, G.239, A.240, G.241 Ligands: ATP.12 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:A.126, B:L.129, B:L.227, B:I.233 Hydrogen bonds: B:N.166 Water bridges: B:A.122, B:N.166 pi-Stacking: B:W.237

4 x K: POTASSIUM ION(Non-covalent)

K.6: 4 residues within 4Å: Chain A: L.22, N.23, P.24, D.26 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:N.23, H2O.1 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.4 K.14: 4 residues within 4Å: Chain B: L.22, N.23, P.24, D.26 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:N.23, H2O.10 K.15: 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.13

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

PEG.8: 7 residues within 4Å: Chain A: E.60, R.68 Chain B: R.68, T.71, R.72, V.75 Ligands: PEG.16 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.60, A:R.68 PEG.16: 7 residues within 4Å: Chain A: R.68, T.71, R.72, V.75 Chain B: E.60, R.68 Ligands: PEG.8 1 PLIP interactions: 1 interactions with chain B Water bridges: 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

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