SMTL ID : 8dqj.1

Crystal structure of pyrrolysyl-tRNA synthetase from Methanomethylophilus alvus engineered for acridone amino acid (AST) bound to ATP and acridone

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.54 Å

Oligo State

homo-dimer

Ligands

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

ATP.1: 21 residues within 4Å: Chain A: R.151, E.153, M.158, H.159, L.160, F.163, M.165, E.219, V.220, C.221, S.222, G.244, F.245, G.246, E.248, R.249, V.260 Ligands: T7Q.2, MG.3, MG.4, MG.5 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:L.160, A:L.160, A:E.219, A:V.220, A:G.246, A:R.249, A:R.249, A:R.249 Water bridges: A:R.151, A:H.159, A:H.159, A:S.222 Salt bridges: A:R.151, A:R.151, A:H.159, A:R.249 pi-Stacking: A:F.163, A:F.163 pi-Cation interactions: A:R.249, A:R.249

1 x T7Q: (2~{S})-2-azanyl-3-(9-oxidanylidene-10~{H}-acridin-2-yl)propanoic acid(Non-covalent)

T7Q.2: 21 residues within 4Å: Chain A: M.121, A.123, L.126, Y.127, M.130, R.151, M.165, S.167, C.169, Y.207, T.210, S.222, A.223, A.224, G.226, T.240, G.242, A.243, G.244 Ligands: ATP.1, MG.3 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:A.123, A:L.126, A:Y.127, A:Y.127, A:Y.207 Hydrogen bonds: A:R.151, A:S.167, A:Y.207, A:Y.207 Water bridges: A:L.122, A:A.123, A:S.222

3 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: E.219, S.222 Ligands: ATP.1, T7Q.2, MG.5 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.219, A:S.222, H2O.2, H2O.4 MG.4: 3 residues within 4Å: Chain A: R.151, H.159 Ligands: ATP.1 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain A: E.219 Ligands: ATP.1, MG.3 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.219, H2O.2, H2O.7

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 12 residues within 4Å: Chain A: M.68, R.84, I.87, R.119, G.147, S.148, T.164 Chain B: R.84, I.87, R.119, G.147, S.148 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:R.119, A:S.148, B:R.84, B:R.119, B:S.148, B:S.148 Water bridges: A:R.84, A:R.84

1 x AMP: ADENOSINE MONOPHOSPHATE(Non-covalent)

AMP.7: 16 residues within 4Å: Chain B: M.121, R.151, E.153, L.160, F.163, M.165, E.219, V.220, C.221, S.222, G.244, F.245, G.246, E.248, R.249, V.260 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:L.160, B:L.160, B:E.219, B:E.219, B:V.220, B:S.222, B:G.246, B:R.249 Water bridges: B:R.151, B:R.151 Salt bridges: B:R.151 pi-Stacking: B:F.163, B:F.163 pi-Cation interactions: B:R.249

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

PEG.8: 7 residues within 4Å: Chain A: W.111, I.112, D.113 Chain B: W.111, I.112, D.113, E.114 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gottfried-Lee, I. et al., Structures of Methanomethylophilus alvus Pyrrolysine tRNA-Synthetases Support the Need for De Novo Selections When Altering the Substrate Specificity. Acs Chem.Biol. (2022)

Release Date

2022-12-07

Peptides

AA_TRNA_LIGASE_II domain-containing protein: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
A

AA_TRNA_LIGASE_II domain-containing protein