SMTL ID : 8dqg.1

Crystal structure of pyrrolysyl-tRNA synthetase from Methanomethylophilus alvus engineered for acridone amino acid (RS1) bound to AMPPNP and acridone

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.49 Å

Oligo State

homo-dimer

Ligands

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 22 residues within 4Å: Chain A: R.151, E.153, M.158, H.159, L.160, E.161, 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 15 PLIP interactions: 15 interactions with chain A Hydrogen bonds: A:R.151, A:E.153, A:H.159, A:L.160, A:V.220, A:V.220, A:G.246, A:R.249, A:R.249, A:R.249 Salt bridges: A:R.151 pi-Stacking: A:F.163, A:F.163 pi-Cation interactions: A:R.249, A:R.249 ANP.8: 19 residues within 4Å: Chain B: M.121, 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 Ligands: MG.9, MG.10 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:R.151, B:E.153, B:E.153, B:H.159, B:L.160, B:E.219, B:V.220, B:S.222, B:G.246, B:R.249, B:R.249, B:R.249 Salt bridges: B:R.151 pi-Stacking: B:F.163, B:F.163 pi-Cation interactions: B:R.249, B: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, L.122, A.123, L.126, Y.127, M.130, R.151, M.165, A.167, G.169, Y.207, T.210, S.222, A.223, A.224, C.240, S.241, G.242, A.243, G.244 Ligands: ANP.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:A.123, A:L.126, A:Y.207, A:Y.207 Hydrogen bonds: A:R.151, A:Y.207, A:Y.207, A:G.242 Water bridges: A:A.123, A:A.123, A:G.242 pi-Stacking: A:Y.127

5 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: E.219, S.222 Ligands: ANP.1, MG.5 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.219, A:S.222, H2O.3 MG.4: 4 residues within 4Å: Chain A: Q.108, R.151, H.159 Ligands: ANP.1 No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain A: E.219 Ligands: ANP.1, MG.3 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.219, H2O.3, H2O.9, H2O.10 MG.9: 3 residues within 4Å: Chain B: E.219, S.222 Ligands: ANP.8 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.219, B:S.222, H2O.18 MG.10: 3 residues within 4Å: Chain B: R.151, H.159 Ligands: ANP.8 No protein-ligand interaction detected (PLIP)

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 9 PLIP interactions: 5 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 Water bridges: A:R.84, A:R.84, A:M.146, B:M.146

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

PEG.7: 7 residues within 4Å: Chain A: W.111, I.112, D.113, E.114 Chain B: W.111, I.112, D.113 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

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