SMTL ID : 6wn2.1

Tyrosyl t-RNA Synthetase Mutant from E.coli Complexed with sulfotyrosine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

homo-dimer

Ligands

2 x TYS: O-SULFO-L-TYROSINE(Non-covalent)

TYS.1: 15 residues within 4Å: Chain A: Y.37, G.39, F.40, D.41, V.71, T.76, D.81, N.126, F.129, Y.175, Q.179, G.182, L.186, Q.195, Q.201 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Q.179 Hydrogen bonds: A:D.81, A:N.126, A:Q.179, A:Q.201 Water bridges: A:G.39, A:G.39, A:D.41, A:R.89, A:G.182, A:G.182 TYS.10: 16 residues within 4Å: Chain B: Y.37, G.39, F.40, D.41, V.71, T.76, D.81, N.126, F.129, Y.175, Q.179, G.182, F.183, L.186, Q.195, Q.201 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:Q.179 Hydrogen bonds: B:Y.37, B:D.81, B:N.126, B:Q.179, B:Q.201 Water bridges: B:D.41, B:D.41, B:R.89, B:D.200

5 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.2: 8 residues within 4Å: Chain A: E.88, E.164, G.167, S.169 Chain B: K.144, H.145, F.146, S.147 2 PLIP interactions: 2 interactions with chain B Water bridges: B:H.145, B:Q.150 PG4.3: 5 residues within 4Å: Chain A: A.44, D.45, W.100, W.245, K.250 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.250 PG4.4: 10 residues within 4Å: Chain A: K.144, H.145, F.146, S.147, Q.150, R.214 Chain B: E.164, G.167, I.168, S.169 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:R.214 Water bridges: B:I.168, B:I.168 PG4.11: 5 residues within 4Å: Chain B: A.44, D.45, W.100, W.245, K.250 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.250 PG4.12: 9 residues within 4Å: Chain B: H.145, F.146, S.147, Q.150, M.151, S.207, D.210, R.213, R.214 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.147, B:S.147, B:R.213 Water bridges: B:D.210, B:D.210

4 x NA: SODIUM ION(Non-functional Binders)

NA.5: 5 residues within 4Å: Chain A: K.154, E.155, W.202, G.203 Ligands: SO4.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.155 Water bridges: A:G.203 NA.6: 5 residues within 4Å: Chain A: I.79, G.80, R.89, L.91, E.172 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.79, A:E.172 NA.13: 4 residues within 4Å: Chain B: I.79, R.89, L.91, E.172 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:I.79 Water bridges: B:S.169 NA.14: 4 residues within 4Å: Chain B: N.5, A.26, L.29, A.30 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.26 Water bridges: B:L.6

7 x SO4: SULFATE ION(Non-functional Binders)

SO4.7: 3 residues within 4Å: Chain A: K.85, A.86, A.87 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.86, A:A.87 Salt bridges: A:K.85 SO4.8: 5 residues within 4Å: Chain A: K.154, W.202, G.203, T.206 Ligands: NA.5 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.154 SO4.9: 4 residues within 4Å: Chain A: T.43, H.48, H.51, R.89 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.43 Salt bridges: A:H.48, A:H.51, A:R.89 SO4.15: 3 residues within 4Å: Chain B: K.85, A.86, A.87 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:A.86, B:A.87 Water bridges: B:K.85, B:K.85 Salt bridges: B:K.85 SO4.16: 4 residues within 4Å: Chain B: K.154, W.202, G.203, T.206 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:W.202, B:T.206 Water bridges: B:K.154 Salt bridges: B:K.154 SO4.17: 4 residues within 4Å: Chain B: T.43, H.48, H.51, R.89 6 PLIP interactions: 6 interactions with chain B Water bridges: B:T.43, B:T.43, B:T.43 Salt bridges: B:H.48, B:H.51, B:R.89 SO4.18: 1 residues within 4Å: Chain B: R.105 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.105

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

He, X. et al., Functional genetic encoding of sulfotyrosine in mammalian cells. Nat Commun (2020)

Release Date

2020-09-02

Peptides

Tyrosine--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Tyrosine--tRNA ligase