SMTL ID : 4cs3.1

Catalytic domain of Pyrrolysyl-tRNA synthetase mutant Y306A, Y384F in complex with an adenylated furan-bearing noncanonical amino acid and pyrophosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

2 x LYS: LYSINE(Non-covalent)

LYS.1: 15 residues within 4Å: Chain A: M.114, A.116, R.144, M.158, N.160, F.198, S.213, A.214, V.215, W.231, G.233, A.234, G.235 Ligands: AMP.2, FU0.3 4 PLIP interactions: 4 interactions with chain A, Hydrophobic interactions: A:F.198 Hydrogen bonds: A:R.144 Water bridges: A:L.115, A:A.116 LYS.8: 15 residues within 4Å: Chain B: M.114, A.116, R.144, M.158, N.160, F.198, S.213, A.214, V.215, W.231, G.233, A.234, G.235 Ligands: AMP.9, FU0.10 4 PLIP interactions: 4 interactions with chain B, Hydrophobic interactions: B:F.198 Hydrogen bonds: B:R.144 Water bridges: B:L.115, B:A.116

2 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.2: 20 residues within 4Å: Chain A: R.144, E.146, H.152, L.153, E.154, F.156, M.158, E.210, L.211, S.212, S.213, G.235, F.236, G.237, E.239, R.240, I.251 Ligands: LYS.1, POP.4, MG.6 17 PLIP interactions: 15 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:E.146, A:L.153, A:E.210, A:E.210, A:E.210, A:S.213, A:G.237, A:R.240, A:R.240 Water bridges: A:H.152, A:H.152, K.1, K.1 Salt bridges: A:R.144 pi-Stacking: A:F.156, A:F.156 pi-Cation interactions: A:R.240 AMP.9: 20 residues within 4Å: Chain B: R.144, E.146, H.152, L.153, E.154, F.156, M.158, E.210, L.211, S.212, S.213, G.235, F.236, G.237, E.239, R.240, I.251 Ligands: LYS.8, POP.11, MG.13 17 PLIP interactions: 15 interactions with chain B, 2 Ligand-Ligand interactions Hydrogen bonds: B:E.146, B:E.146, B:L.153, B:E.210, B:E.210, B:S.213, B:G.237, B:R.240, B:R.240 Water bridges: B:H.152, B:H.152, K.8, K.8 Salt bridges: B:R.144 pi-Stacking: B:F.156, B:F.156 pi-Cation interactions: B:R.240

2 x FU0: 2-(FURAN-2-YL)ETHYL HYDROGEN CARBONATE(Non-covalent)

FU0.3: 16 residues within 4Å: Chain A: M.90, A.116, L.119, A.120, L.123, N.160, C.162, F.198, I.219, L.221, D.222, I.227, W.231, G.233, A.234 Ligands: LYS.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.227 Hydrogen bonds: A:N.160 pi-Stacking: A:W.231 FU0.10: 16 residues within 4Å: Chain B: M.90, A.116, L.119, A.120, L.123, N.160, C.162, F.198, I.219, L.221, D.222, I.227, W.231, G.233, A.234 Ligands: LYS.8 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.227 Hydrogen bonds: B:N.160 pi-Stacking: B:W.231

2 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.4: 8 residues within 4Å: Chain A: R.144, H.152, E.210, S.213, R.240 Ligands: AMP.2, MG.5, MG.6 7 PLIP interactions: 7 interactions with chain A Water bridges: A:R.144, A:E.146, A:H.152, A:H.152 Salt bridges: A:R.144, A:H.152, A:R.240 POP.11: 8 residues within 4Å: Chain B: R.144, H.152, E.210, S.213, R.240 Ligands: AMP.9, MG.12, MG.13 8 PLIP interactions: 8 interactions with chain B Water bridges: B:R.144, B:E.146, B:E.151, B:H.152, B:H.152 Salt bridges: B:R.144, B:H.152, B:R.240

4 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.5: 4 residues within 4Å: Chain A: Q.101, R.144, H.152 Ligands: POP.4 No protein-ligand interaction detected (PLIP) MG.6: 4 residues within 4Å: Chain A: E.210, S.213 Ligands: AMP.2, POP.4 5 PLIP interactions: 2 interactions with chain A, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: A:E.210, A:S.213, AMP.2, H2O.8, H2O.9 MG.12: 4 residues within 4Å: Chain B: Q.101, R.144, H.152 Ligands: POP.11 No protein-ligand interaction detected (PLIP) MG.13: 4 residues within 4Å: Chain B: E.210, S.213 Ligands: AMP.9, POP.11 5 PLIP interactions: 2 interactions with chain B, 1 Ligand-Ligand interactions, 2 Ligand-Water interactions Metal complexes: B:E.210, B:S.213, AMP.9, H2O.18, H2O.18

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

EDO.7: 14 residues within 4Å: Chain A: N.55, Y.56, L.57, L.242, F.248, R.253, A.254, A.255, R.256, Y.260, Y.261, N.262, G.263 Chain B: K.77 8 PLIP interactions: 6 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:N.55, A:N.262, A:G.263 Water bridges: A:N.55, A:A.255, A:Y.260, B:K.77, B:K.77 EDO.14: 14 residues within 4Å: Chain A: K.77 Chain B: N.55, Y.56, L.57, L.242, F.248, R.253, A.254, A.255, R.256, Y.260, Y.261, N.262, G.263 8 PLIP interactions: 6 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:N.55, B:N.262, B:G.263 Water bridges: B:N.55, B:A.255, B:Y.260, A:K.77, A:K.77

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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