SMTL ID : 2haw.1

Crystal structure of family II Inorganic pyrophosphatase in complex with PNP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-dimer

Ligands

8 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 7 residues within 4Å: Chain A: H.9, D.13, D.75 Ligands: MG.2, MG.4, F.5, 2PN.10 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.9, A:D.13, A:D.13, A:D.75 MG.2: 8 residues within 4Å: Chain A: D.15, D.75, H.97, D.149 Ligands: MG.1, MG.4, F.5, 2PN.10 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.15, A:D.75, A:H.97, A:D.149 MG.3: 5 residues within 4Å: Chain A: D.13, R.295 Ligands: MG.4, SO4.7, 2PN.10 No protein-ligand interaction detected (PLIP) MG.4: 7 residues within 4Å: Chain A: D.13, D.149 Ligands: MG.1, MG.2, MG.3, F.5, 2PN.10 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.13, A:D.149, H2O.1, H2O.2 MG.11: 8 residues within 4Å: Chain B: H.9, D.13, T.16, D.75 Ligands: MG.12, MG.14, F.15, 2PN.20 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.9, B:D.13, B:D.13, B:D.75 MG.12: 8 residues within 4Å: Chain B: D.15, D.75, H.97, D.149 Ligands: MG.11, MG.14, F.15, 2PN.20 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.15, B:D.75, B:H.97, B:D.149 MG.13: 5 residues within 4Å: Chain B: D.13, R.295 Ligands: MG.14, SO4.17, 2PN.20 No protein-ligand interaction detected (PLIP) MG.14: 7 residues within 4Å: Chain B: D.13, D.149 Ligands: MG.11, MG.12, MG.13, F.15, 2PN.20 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.13, B:D.149, H2O.7, H2O.10

2 x F: FLUORIDE ION(Non-covalent)

F.5: 8 residues within 4Å: Chain A: D.13, D.15, D.75, D.149 Ligands: MG.1, MG.2, MG.4, 2PN.10 No protein-ligand interaction detected (PLIP) F.15: 8 residues within 4Å: Chain B: D.13, D.15, D.75, D.149 Ligands: MG.11, MG.12, MG.14, 2PN.20 No protein-ligand interaction detected (PLIP)

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

SO4.6: 3 residues within 4Å: Chain A: R.38, Q.41, L.60 2 PLIP interactions: 2 interactions with chain A Water bridges: A:V.42 Salt bridges: A:R.38 SO4.7: 6 residues within 4Å: Chain A: H.98, K.205, R.295, K.296 Ligands: MG.3, 2PN.10 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.296 Water bridges: A:R.295, A:R.295 Salt bridges: A:H.98, A:K.205, A:R.295, A:K.296 SO4.16: 3 residues within 4Å: Chain B: R.38, Q.41, L.60 3 PLIP interactions: 3 interactions with chain B Water bridges: B:R.38, B:V.42 Salt bridges: B:R.38 SO4.17: 6 residues within 4Å: Chain B: H.98, K.205, R.295, K.296 Ligands: MG.13, 2PN.20 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:R.295, B:K.296 Water bridges: B:D.203, B:D.203, B:D.203, B:Q.218 Salt bridges: B:H.98, B:K.205, B:R.295, B:K.296

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.8: 2 residues within 4Å: Chain A: E.56, S.57 Ligand excluded by PLIP

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

PG4.9: 8 residues within 4Å: Chain A: Y.23, K.27, L.30, F.32, E.93, Y.110, M.126, N.130 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.27, A:E.93 PG4.19: 3 residues within 4Å: Chain B: M.1, E.2, N.33 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:M.1

2 x 2PN: IMIDODIPHOSPHORIC ACID(Non-covalent)

2PN.10: 15 residues within 4Å: Chain A: H.9, D.13, D.75, H.97, H.98, D.149, K.205, R.295, K.296 Ligands: MG.1, MG.2, MG.3, MG.4, F.5, SO4.7 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:K.205, A:R.295, A:R.295, A:K.296, A:K.296, A:K.296 Water bridges: A:D.13, A:D.13, A:D.203 2PN.20: 15 residues within 4Å: Chain B: H.9, D.13, D.75, H.97, H.98, D.149, K.205, R.295, K.296 Ligands: MG.11, MG.12, MG.13, MG.14, F.15, SO4.17 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:D.149, B:D.149, B:K.205, B:R.295, B:R.295, B:K.296, B:K.296, B:K.296 Water bridges: B:D.149, B:D.203, B:D.203

1 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.18: 10 residues within 4Å: Chain B: I.4, Y.23, K.27, L.30, F.32, L.92, E.93, Y.110, M.126, N.130 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.27, B:E.93

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.21: 4 residues within 4Å: Chain B: K.133, E.135, K.136, E.137 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.133, B:K.136, B:E.137 Water bridges: B:E.135, B:E.135 GOL.22: 5 residues within 4Å: Chain B: T.195, V.196, E.197, R.230, E.233 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:V.196, B:E.197, B:R.230, B:R.230 GOL.23: 3 residues within 4Å: Chain B: Q.47, E.56, S.57 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.47, B:E.56, B:S.57 Water bridges: B:D.51, B:D.51

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fabrichniy, I.P. et al., A trimetal site and substrate distortion in a family II inorganic pyrophosphatase. J.Biol.Chem. (2007)

Release Date

2006-11-14

Peptides

Manganese-dependent inorganic pyrophosphatase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Manganese-dependent inorganic pyrophosphatase

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