SMTL ID : 2dxw.1 (1 other biounit)

Crystal structure of Glu54 to Lys mutant of Diphthine synthase

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 3 residues within 4Å: Chain A: R.60, A.91, T.93 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.60, A:E.64, A:T.93, A:T.93 Salt bridges: A:R.60 SO4.2: 4 residues within 4Å: Chain A: Y.11, S.211, L.212, N.213 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.11, A:Y.11, A:L.212, A:N.213, A:N.213 SO4.3: 2 residues within 4Å: Chain A: P.257, R.258 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.258 Water bridges: A:E.259 SO4.7: 3 residues within 4Å: Chain B: H.126, Y.128, H.243 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.128, B:Y.128 Water bridges: B:H.126 Salt bridges: B:H.126, B:H.243 SO4.8: 4 residues within 4Å: Chain B: K.129, K.241, L.242, H.243 7 PLIP interactions: 7 interactions with chain B Water bridges: B:Y.128, B:K.129, B:K.129, B:K.241, B:I.244 Salt bridges: B:K.129, B:K.241 SO4.9: 2 residues within 4Å: Chain B: P.257, R.258 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.258 Salt bridges: B:R.258 SO4.10: 4 residues within 4Å: Chain B: R.60, A.91, T.92, T.93 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.93 Water bridges: B:T.92, B:T.92 Salt bridges: B:R.60

1 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.4: 19 residues within 4Å: Chain A: L.10, T.36, S.37, P.85, G.86, D.87, V.90, A.91, T.92, S.115, I.116, F.165, L.166, L.206, R.208, A.209, P.233, H.234, I.235 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.37, A:D.87, A:V.90, A:I.116, A:L.166, A:L.166, A:R.208, A:A.209, A:A.209 Water bridges: A:S.37, A:L.166

2 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.5: 7 residues within 4Å: Chain A: F.34, M.39, T.42, T.43, L.44, I.47, V.57 2 PLIP interactions: 2 interactions with chain A Water bridges: A:L.44, A:L.44 MES.11: 4 residues within 4Å: Chain B: D.200, Y.220, K.222, E.259 5 PLIP interactions: 5 interactions with chain B Water bridges: B:K.222, B:E.259 Salt bridges: B:D.200, B:K.222, B:E.259

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 2 residues within 4Å: Chain A: T.43, R.46 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.43, A:T.43 Water bridges: A:T.43, A:L.44 GOL.12: 7 residues within 4Å: Chain B: F.34, L.38, M.39, T.42, T.43, L.44, R.173 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:M.39, B:L.44, B:R.173 GOL.13: 5 residues within 4Å: Chain A: Y.128, K.129, L.160, H.243 Chain B: K.132 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.132, A:G.159 Water bridges: B:K.132, A:K.129 GOL.14: 5 residues within 4Å: Chain A: Y.128 Chain B: S.133, A.134, T.135, F.165 1 PLIP interactions: 1 interactions with chain B Water bridges: B:T.135

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mizutani, H. et al., Crystal structure of diphthine synthase from Pyrococcus horikoshii OT3. To be Published

Release Date

2007-03-01

Peptides

diphthine synthase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

diphthine synthase

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