SMTL ID : 2dvn.1

Structure of PH1917 protein with the complex of IMP from Pyrococcus horikoshii

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

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

SO4.1: 4 residues within 4Å: Chain A: N.9, S.82, R.86 Ligands: IMP.14 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.9, A:S.82, A:S.82 Salt bridges: A:R.86 SO4.2: 8 residues within 4Å: Chain A: T.7, S.8, N.9, K.12, Y.34, E.36, E.64 Ligands: IMP.14 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.8, A:N.9, A:Y.34, A:E.36 Water bridges: A:N.9 Salt bridges: A:K.12 SO4.3: 4 residues within 4Å: Chain A: K.41, F.69, Y.106, K.108 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.43, A:Y.106, A:Y.106 Water bridges: A:K.41, A:K.41, A:K.108 Salt bridges: A:K.41, A:K.108 SO4.4: 4 residues within 4Å: Chain A: Y.85, R.86, F.140, G.141 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.85, A:Y.85, A:G.141 Water bridges: A:R.86, A:R.86 Salt bridges: A:R.86 SO4.5: 7 residues within 4Å: Chain A: R.14, H.138, T.159, I.160 Chain B: W.179, N.183 Ligands: GOL.16 6 PLIP interactions: 2 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:W.179, B:N.183, A:I.160 Water bridges: A:G.139 Salt bridges: A:R.14, A:H.138 SO4.6: 4 residues within 4Å: Chain A: G.89, L.90, E.91, K.134 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.90, A:E.91 Water bridges: A:Y.85 Salt bridges: A:K.134 SO4.7: 6 residues within 4Å: Chain A: R.129, S.131, N.132, E.133, R.135, I.147 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.132, A:N.132, A:E.133 Water bridges: A:R.129, A:R.129 Salt bridges: A:R.129, A:R.135 SO4.8: 4 residues within 4Å: Chain A: N.164, A.165, G.170, K.174 3 PLIP interactions: 3 interactions with chain A Water bridges: A:A.165, A:A.165 Salt bridges: A:K.174 SO4.9: 3 residues within 4Å: Chain A: H.32, W.52, K.56 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.52 Salt bridges: A:H.32, A:K.56 SO4.10: 4 residues within 4Å: Chain B: G.89, L.90, E.91, K.134 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:L.90, B:E.91 Water bridges: B:K.134 Salt bridges: B:K.134 SO4.11: 5 residues within 4Å: Chain B: S.72, G.99, A.100, E.101, D.102 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.72, B:E.101, B:D.102 SO4.12: 3 residues within 4Å: Chain B: Y.85, F.140, G.141 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Y.85, B:G.141 SO4.13: 3 residues within 4Å: Chain B: S.151, E.152, K.153 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.151, B:E.152, B:K.153 Water bridges: B:E.152

2 x IMP: INOSINIC ACID(Non-covalent)

IMP.14: 18 residues within 4Å: Chain A: 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: SO4.1, SO4.2 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:D.65, A:D.65, A:S.66, A:S.66, A:S.81, A:Y.142, A:D.143, A:D.143, A:K.163, A:R.169, A:R.169 Water bridges: A:S.82, A:S.82 Salt bridges: A:K.12 IMP.15: 15 residues within 4Å: Chain B: K.12, E.64, D.65, S.66, G.67, S.81, S.82, F.107, F.140, G.141, Y.142, D.143, K.163, H.168, R.169 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:E.64, B:S.66, B:S.66, B:S.82, B:Y.142, B:D.143, B:K.163, B:R.169 Water bridges: B:N.9, B:K.12 Salt bridges: B:K.12, B:R.169 pi-Stacking: B:F.140

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.16: 6 residues within 4Å: Chain A: R.14, H.138, G.139 Chain B: E.178, W.179 Ligands: SO4.5 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:R.14, A:H.138, A:G.139, B:E.178 GOL.17: 7 residues within 4Å: Chain B: T.7, S.8, N.9, K.12, Y.34, E.36, E.64 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.8, B:S.8, B:E.64 Water bridges: B:N.9, B:K.12, B:Y.34 GOL.18: 2 residues within 4Å: Chain A: V.125, K.171 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.171, A:K.171

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lokanath, N.K. et al., Structures of dimeric nonstandard nucleotide triphosphate pyrophosphatase from Pyrococcus horikoshii OT3: functional significance of interprotomer conformational changes. J.Mol.Biol. (2008)

Release Date

2007-09-04

Peptides

Hypothetical protein PH1917: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Hypothetical protein PH1917

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