SMTL ID : 2eh2.2 (2 other biounits)

Mutant V18M structure of PH0725 from Pyrococcus horikoshii OT3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-tetramer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: T.36, R.60, A.91, T.92 6 PLIP interactions: 6 interactions with chain A Water bridges: A:T.36, A:R.60, A:R.60, A:R.60, A:T.93 Salt bridges: A:R.60 SO4.4: 4 residues within 4Å: Chain B: K.129, K.241, L.242, H.243 6 PLIP interactions: 6 interactions with chain B Water bridges: B:Y.128, B:K.129, B:K.129, B:I.244 Salt bridges: B:K.129, B:K.241 SO4.5: 4 residues within 4Å: Chain D: W.143, P.145, T.146, S.147 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:T.146, D:S.147 Water bridges: D:S.147, D:S.147 SO4.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) SO4.10: 4 residues within 4Å: Chain C: T.36, R.60, A.91, T.92 6 PLIP interactions: 6 interactions with chain C Water bridges: C:Y.35, C:T.36, C:R.60, C:R.60, C:T.93 Salt bridges: C:R.60 SO4.13: 4 residues within 4Å: Chain D: K.129, K.241, L.242, H.243 7 PLIP interactions: 7 interactions with chain D Water bridges: D:Y.128, D:Y.128, D:K.129, D:K.129, D:I.244 Salt bridges: D:K.129, D:K.241 SO4.14: 4 residues within 4Å: Chain B: W.143, P.145, T.146, S.147 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.146, B:S.147 Water bridges: B:T.146, B:S.147, B:S.147 SO4.15: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

SAH.2: 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 12 PLIP interactions: 12 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.38, A:L.166 SAH.11: 19 residues within 4Å: Chain C: 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 12 PLIP interactions: 12 interactions with chain C Hydrogen bonds: C:S.37, C:D.87, C:V.90, C:I.116, C:L.166, C:L.166, C:R.208, C:A.209, C:A.209 Water bridges: C:S.37, C:L.38, C:L.166

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

MES.3: 7 residues within 4Å: Chain A: F.34, M.39, T.42, T.43, L.44, I.47, V.57 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.44 Water bridges: A:M.39 pi-Cation interactions: A:F.34 MES.7: 6 residues within 4Å: Chain B: T.177, N.179, E.180, R.226, E.227, D.228 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.177, B:E.180 Water bridges: B:N.179, B:I.225 MES.8: 9 residues within 4Å: Chain B: G.9, T.36, S.37, P.85, G.86, A.91, S.115, I.116, F.165 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:S.37, B:P.85, B:I.116 Water bridges: B:L.10, B:S.37, B:S.37, B:L.38, B:D.87, B:D.87 MES.9: 3 residues within 4Å: Chain B: D.200, Y.220, E.259 3 PLIP interactions: 3 interactions with chain B Water bridges: B:D.200 Salt bridges: B:D.200, B:E.259 MES.12: 7 residues within 4Å: Chain C: F.34, M.39, T.42, T.43, L.44, I.47, V.57 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:L.44 Water bridges: C:M.39 pi-Cation interactions: C:F.34 MES.16: 6 residues within 4Å: Chain D: T.177, N.179, E.180, R.226, E.227, D.228 2 PLIP interactions: 2 interactions with chain D Water bridges: D:N.179, D:I.225 MES.17: 9 residues within 4Å: Chain D: G.9, T.36, S.37, P.85, G.86, A.91, S.115, I.116, F.165 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:S.37, D:P.85, D:I.116 Water bridges: D:L.10, D:S.37, D:S.37, D:L.38, D:D.87, D:D.87 MES.18: 3 residues within 4Å: Chain D: D.200, Y.220, E.259 2 PLIP interactions: 2 interactions with chain D Salt bridges: D:D.200, D:E.259

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shimizu, K. et al., Mutant V18M structure of PH0725 from Pyrococcus horikoshii OT3. To be Published

Release Date

2007-09-04

Peptides

diphthine synthase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

diphthine synthase

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