SMTL ID : 4bwa.1

PylRS Y306G, Y384F, I405R mutant in complex with adenylated norbornene

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 3 residues within 4Å: Chain A: E.233, S.236 Ligands: N0B.2 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.233, A:S.236, H2O.2 MG.6: 3 residues within 4Å: Chain B: E.233, S.236 Ligands: N0B.7 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.233, B:S.236, H2O.3

2 x N0B: Adenylated Norbornene(Non-covalent)

N0B.2: 26 residues within 4Å: Chain A: M.137, A.139, G.143, L.146, R.167, E.169, E.174, H.175, L.176, F.179, M.181, N.183, C.185, E.233, L.234, S.235, S.236, V.238, D.245, W.254, G.256, A.257, G.258, G.260, R.263 Ligands: MG.1 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:A.139, A:L.146, A:V.238, A:W.254, A:W.254 Hydrogen bonds: A:L.176, A:L.176, A:E.233, A:L.234, A:S.236, A:G.260, A:R.263 Water bridges: A:A.139, A:R.167 Salt bridges: A:R.167, A:R.167 pi-Stacking: A:F.179, A:F.179 N0B.7: 26 residues within 4Å: Chain B: M.137, A.139, G.143, L.146, R.167, E.169, E.174, H.175, L.176, F.179, M.181, N.183, C.185, E.233, L.234, S.235, S.236, V.238, D.245, W.254, G.256, A.257, G.258, G.260, R.263 Ligands: MG.6 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:A.139, B:L.146, B:V.238, B:W.254, B:W.254 Hydrogen bonds: B:L.176, B:L.176, B:E.233, B:L.234, B:S.236, B:G.260, B:R.263 Water bridges: B:A.139, B:R.167 Salt bridges: B:R.167, B:R.167 pi-Stacking: B:F.179, B:F.179

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

PEG.3: 10 residues within 4Å: Chain A: L.80, E.84, K.100, I.162, G.163, P.164, T.180, R.279 Chain B: R.279 Ligands: PEG.8 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:R.279, B:R.279, A:L.80, A:R.279 PEG.8: 10 residues within 4Å: Chain A: R.279 Chain B: L.80, E.84, K.100, I.162, G.163, P.164, T.180, R.279 Ligands: PEG.3 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:L.80, B:R.279, A:R.279, A:R.279

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

EDO.4: 7 residues within 4Å: Chain A: Y.79, K.82, L.83, E.86, L.265, K.268, H.269 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.86, A:K.268, A:H.269 EDO.5: 7 residues within 4Å: Chain A: N.78, R.276, A.277, A.278, Y.283, N.285, G.286 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.78, A:A.277, A:N.285, A:G.286 EDO.9: 7 residues within 4Å: Chain B: Y.79, K.82, L.83, E.86, L.265, K.268, H.269 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.86, B:K.268, B:H.269 EDO.10: 7 residues within 4Å: Chain B: N.78, R.276, A.277, A.278, Y.283, N.285, G.286 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.78, B:A.277, B:N.285, B:G.286

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Schneider, S. et al., Structural Insights Into Incorporation of Norbornene Amino Acids for Click Modification of Proteins. Chem.Bio.Chem. (2013)

Release Date

2013-07-31

Peptides

PYRROLYSINE--TRNA LIGASE: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

PYRROLYSINE--TRNA LIGASE

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