SMTL ID : 2e5x.1

Structure of nucleotide triphosphate pyrophosphatase from pyrococcus horikoshii OT3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

NA.1: 7 residues within 4Å: Chain A: Y.34, E.36, E.64, D.65 Ligands: NA.2, NA.3, ITT.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.36, A:E.64 Water bridges: A:E.64 NA.2: 4 residues within 4Å: Chain A: E.36 Ligands: NA.1, NA.3, ITT.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.36 NA.3: 5 residues within 4Å: Chain A: E.36, D.65 Ligands: NA.1, NA.2, ITT.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.65 Water bridges: A:E.36, A:S.66 NA.7: 7 residues within 4Å: Chain B: Y.34, E.36, E.64, D.65 Ligands: NA.8, NA.9, ITT.10 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.34, B:E.36, B:D.65 Water bridges: B:T.7 NA.8: 4 residues within 4Å: Chain B: E.36 Ligands: NA.7, NA.9, ITT.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.36 NA.9: 5 residues within 4Å: Chain B: E.36, D.65 Ligands: NA.7, NA.8, ITT.10 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.65 Water bridges: B:S.66

2 x ITT: INOSINE 5'-TRIPHOSPHATE(Non-covalent)

ITT.4: 22 residues within 4Å: Chain A: T.7, S.8, N.9, K.12, E.36, E.64, D.65, S.66, S.81, S.82, Y.85, F.107, F.140, G.141, Y.142, D.143, K.163, H.168, R.169 Ligands: NA.1, NA.2, NA.3 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:S.8, A:N.9, A:E.36, A:E.64, A:S.66, A:S.66, A:S.82, A:S.82, A:Y.142, A:D.143, A:K.163, A:R.169, A:R.169 Water bridges: A:Y.34, A:E.36, A:S.82, A:S.82 Salt bridges: A:K.12, A:K.12, A:K.12 ITT.10: 22 residues within 4Å: Chain B: T.7, S.8, N.9, K.12, E.36, E.64, D.65, S.66, S.81, S.82, Y.85, F.107, F.140, G.141, Y.142, D.143, K.163, H.168, R.169 Ligands: NA.7, NA.8, NA.9 21 PLIP interactions: 21 interactions with chain B Hydrogen bonds: B:T.7, B:S.8, B:N.9, B:E.36, B:E.64, B:D.65, B:S.66, B:S.66, B:S.82, B:S.82, B:Y.142, B:D.143, B:K.163, B:R.169, B:R.169 Water bridges: B:Y.34, B:S.82, B:S.82 Salt bridges: B:K.12, B:K.12, B:K.12

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

EDO.5: 3 residues within 4Å: Chain A: E.43, K.121, S.123 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:E.43, A:E.43, A:S.123 Water bridges: A:K.121, A:S.123, A:S.123, A:S.123 EDO.6: 6 residues within 4Å: Chain A: F.69, I.70, E.71, G.75, Y.106, W.127 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.71 EDO.11: 3 residues within 4Å: Chain B: E.43, K.121, S.123 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.43, B:S.123 Water bridges: B:K.121, B:S.123, B:S.123, B:S.123 EDO.12: 6 residues within 4Å: Chain B: F.69, I.70, E.71, G.75, Y.106, W.127 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.71, B:E.71

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mizutani, H. et al., Structure of nucleotide triphosphate pyrophosphatase from pyrococcus horikoshii OT3. To be Published

Release Date

2007-06-26

Peptides

Hypothetical protein PH1917: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Hypothetical protein PH1917