SMTL ID : 6aaz.1

Crystal structure of Methanosarcina mazei PylRS(Y306A/Y384F) complexed with pNO2ZLys

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.84 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 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.216, A:S.219, H2O.5, H2O.6 MG.3: 3 residues within 4Å: Chain A: E.216 Ligands: MG.2, ATP.4 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.216, H2O.5, H2O.5 MG.10: 2 residues within 4Å: Chain B: H.158 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.15, H2O.17 MG.12: 3 residues within 4Å: Chain B: E.216 Ligands: MG.11, ATP.13 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.216, H2O.15, H2O.15

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

ATP.4: 17 residues within 4Å: Chain A: R.150, E.152, 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, 9UC.5 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:R.150, A:E.152, A:L.159, A:E.216, A:S.219, A:G.243, A:R.246 Water bridges: A:E.157, A:L.247 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: 17 residues within 4Å: Chain B: R.150, E.152, 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, 9UC.14 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:R.150, B:E.152, B:E.152, B:L.159, B:E.216, B:S.219, B:G.243, B:R.246 Water bridges: B:E.157, B:L.247 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 9UC: N6-{[(4-nitrophenyl)methoxy]carbonyl}-L-lysine(Non-covalent)

9UC.5: 20 residues within 4Å: Chain A: M.96, A.122, A.126, L.129, R.150, M.164, N.166, F.167, C.168, F.204, S.219, L.227, D.228, W.231, I.233, W.237, G.239, A.240, G.241 Ligands: ATP.4 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:A.122, A:A.126, A:F.204, A:I.233, A:W.237, A:W.237 Hydrogen bonds: A:R.150, A:N.166, A:A.240 9UC.14: 20 residues within 4Å: Chain B: M.96, A.122, A.126, L.129, R.150, M.164, N.166, F.167, C.168, F.204, S.219, L.227, D.228, W.231, I.233, W.237, G.239, A.240, G.241 Ligands: ATP.13 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:A.122, B:A.126, B:F.204, B:I.233, B:W.237, B:W.237 Hydrogen bonds: B:R.150, B:N.166, B:A.240

2 x CIT: CITRIC ACID(Non-functional Binders)

CIT.6: 4 residues within 4Å: Chain A: R.130, K.131, R.134 Chain B: N.273 9 PLIP interactions: 8 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.130, A:K.131, B:N.273 Water bridges: A:R.134, A:R.134 Salt bridges: A:R.130, A:K.131, A:K.131, A:R.134 CIT.15: 4 residues within 4Å: Chain A: N.273 Chain B: R.130, K.131, R.134 9 PLIP interactions: 1 interactions with chain A, 8 interactions with chain B Hydrogen bonds: A:N.273, B:R.130, B:K.131 Water bridges: B:R.134, B:R.134 Salt bridges: B:R.130, B:K.131, B:K.131, B:R.134

6 x K: POTASSIUM ION(Non-covalent)

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.7 K.8: 2 residues within 4Å: Chain A: R.37, E.38 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.38 K.9: 2 residues within 4Å: Chain A: D.253, K.255 No protein-ligand interaction detected (PLIP) 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.17 K.17: 2 residues within 4Å: Chain B: R.37, E.38 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.38 K.18: 2 residues within 4Å: Chain B: D.253, K.255 No protein-ligand interaction detected (PLIP)

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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