SMTL ID : 8c49.1

Crystal structure of pyrrolysyl-tRNA synthetase from Methanomethylophilus alvus engineered for 3-Methyl-L-histidine, bound to AMPPNP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.82 Å

Oligo State

homo-dimer

Ligands

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

ANP.1: 22 residues within 4Å: Chain A: M.120, R.150, E.152, M.157, H.158, L.159, F.162, M.164, E.218, V.219, C.220, S.221, G.243, F.244, G.245, E.247, R.248, V.259 Ligands: PGE.5, MG.9, MG.10, MG.11 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:R.150, A:H.158, A:L.159, A:L.159, A:E.218, A:E.218, A:S.221, A:G.245, A:R.248, A:R.248, A:R.248 Water bridges: A:Q.107, A:E.218, A:E.218 Salt bridges: A:R.150 pi-Stacking: A:F.162, A:F.162 pi-Cation interactions: A:R.248, A:R.248 ANP.15: 21 residues within 4Å: Chain B: R.150, E.152, M.157, H.158, L.159, F.162, M.164, E.218, V.219, C.220, S.221, G.243, F.244, G.245, E.247, R.248, V.259 Ligands: PGE.21, MG.22, MG.23, MG.24 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:R.150, B:E.152, B:H.158, B:L.159, B:E.218, B:E.218, B:E.218, B:S.221, B:G.245, B:R.248, B:R.248, B:R.248 Water bridges: B:E.152, B:T.209, B:D.211, B:S.221 Salt bridges: B:R.150 pi-Stacking: B:F.162, B:F.162 pi-Cation interactions: B:R.248, B:R.248

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

PEG.2: 6 residues within 4Å: Chain A: K.50, G.53, M.54, N.57, S.59, N.270 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.50 PEG.6: 6 residues within 4Å: Chain A: T.177, K.181, L.198, V.199, Q.200, I.210 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.181 PEG.7: 15 residues within 4Å: Chain A: R.60, T.64, M.67, N.68, R.83, M.145 Chain B: R.60, T.64, M.67, N.68, A.71, E.81, R.83, F.143, M.145 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.60, A:R.60, A:R.60 PEG.8: 8 residues within 4Å: Chain A: W.110, I.111, D.112 Chain B: W.110, I.111, D.112, E.113 Ligands: PEG.19 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.112 PEG.14: 5 residues within 4Å: Chain A: D.134, H.135, T.136, D.137 Chain B: K.52 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.52 PEG.17: 6 residues within 4Å: Chain B: E.77, R.173, V.179, N.182, Y.183, V.186 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:N.182 Water bridges: B:K.141, B:K.141, B:D.169, B:Y.183 PEG.19: 7 residues within 4Å: Chain B: K.90, E.100, F.105, W.110, D.112, E.113 Ligands: PEG.8 No protein-ligand interaction detected (PLIP)

3 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.3: 13 residues within 4Å: Chain A: Y.16, G.17, N.18, A.43, D.46, N.47, K.50, E.254, K.255, Y.256, G.271, A.272, K.273 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.18, A:N.18 PGE.5: 20 residues within 4Å: Chain A: M.120, A.122, I.125, F.126, R.150, M.164, N.166, L.167, F.168, F.206, S.221, A.222, A.223, W.239, S.240, G.241, A.242, G.243 Ligands: ANP.1, MG.12 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.166 PGE.21: 19 residues within 4Å: Chain B: M.120, A.122, I.125, F.126, R.150, M.164, N.166, L.167, F.168, F.206, S.221, A.222, A.223, W.239, G.241, A.242, G.243 Ligands: ANP.15, MG.27 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.166, B:A.242

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

EDO.4: 4 residues within 4Å: Chain A: P.226, H.227, Y.228, D.230 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.227 Water bridges: A:D.230 EDO.16: 5 residues within 4Å: Chain B: H.227, Y.228, L.229, D.230, A.231 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.230, B:A.231 EDO.18: 3 residues within 4Å: Chain B: T.6, A.8, Q.9 1 PLIP interactions: 1 interactions with chain B Water bridges: B:A.8 EDO.20: 9 residues within 4Å: Chain B: K.50, M.54, S.59, R.60, G.62, Q.65, E.254, Y.256, N.270 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.50, B:S.59 Water bridges: B:E.254, B:E.254

11 x MG: MAGNESIUM ION(Non-covalent)

MG.9: 4 residues within 4Å: Chain A: Q.107, R.150, H.158 Ligands: ANP.1 No protein-ligand interaction detected (PLIP) MG.10: 4 residues within 4Å: Chain A: D.211, E.218, S.221 Ligands: ANP.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.218, A:S.221, H2O.2, H2O.4 MG.11: 2 residues within 4Å: Chain A: E.218 Ligands: ANP.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.218, H2O.4, H2O.4, H2O.4, H2O.5 MG.12: 7 residues within 4Å: Chain A: M.120, L.121, A.122, M.164, N.166, G.243 Ligands: PGE.5 No protein-ligand interaction detected (PLIP) MG.13: 7 residues within 4Å: Chain A: P.139, K.141, D.169, P.172, R.173, V.179, Y.183 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.169, H2O.3, H2O.3 MG.22: 3 residues within 4Å: Chain B: R.150, H.158 Ligands: ANP.15 No protein-ligand interaction detected (PLIP) MG.23: 5 residues within 4Å: Chain B: T.209, D.211, E.218, S.221 Ligands: ANP.15 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:E.218, B:S.221, H2O.5, H2O.8 MG.24: 2 residues within 4Å: Chain B: E.218 Ligands: ANP.15 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.218, H2O.6, H2O.7, H2O.7, H2O.9 MG.25: 1 residues within 4Å: Chain B: D.69 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.69, H2O.5, H2O.9, H2O.9, H2O.10 MG.26: 5 residues within 4Å: Chain B: I.10, R.14, T.20, Y.21, E.22 No protein-ligand interaction detected (PLIP) MG.27: 7 residues within 4Å: Chain B: M.120, L.121, A.122, M.164, N.166, G.243 Ligands: PGE.21 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Taylor, C.J. et al., Engineering mutually orthogonal PylRS/tRNA pairs for dual encoding of functional histidine analogues. Protein Sci. (2023)

Release Date

2023-07-19

Peptides

Pyrrolysyl-tRNA synthetase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Pyrrolysyl-tRNA synthetase