SMTL ID : 2auu.1

Inorganic pyrophosphatase complexed with magnesium pyrophosphate and fluoride

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.22 Å

Oligo State

homo-hexamer

Ligands

24 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 9 residues within 4Å: Chain A: D.65, D.67, D.70, D.102, K.104 Ligands: MG.2, MG.3, F.9, POP.10 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.65, A:D.70, A:D.102, H2O.1 MG.2: 6 residues within 4Å: Chain A: Y.55, D.67, D.70 Ligands: MG.1, F.9, POP.10 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.70, H2O.1, H2O.1, H2O.3 MG.3: 7 residues within 4Å: Chain A: D.65, D.97, D.102, K.104, K.142 Ligands: MG.1, POP.10 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.97, A:D.102, H2O.3, H2O.3 MG.4: 4 residues within 4Å: Chain A: K.29, E.31, D.67 Ligands: POP.10 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.31, H2O.3, H2O.7, H2O.7 MG.11: 9 residues within 4Å: Chain B: D.65, D.67, D.70, D.102, K.104 Ligands: MG.12, MG.13, F.19, POP.20 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.65, B:D.70, B:D.102, H2O.9 MG.12: 6 residues within 4Å: Chain B: Y.55, D.67, D.70 Ligands: MG.11, F.19, POP.20 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.70, H2O.8, H2O.8, H2O.10 MG.13: 7 residues within 4Å: Chain B: D.65, D.97, D.102, K.104, K.142 Ligands: MG.11, POP.20 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.97, B:D.102, H2O.10, H2O.10 MG.14: 4 residues within 4Å: Chain B: K.29, E.31, D.67 Ligands: POP.20 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.31, H2O.11, H2O.15, H2O.15 MG.21: 9 residues within 4Å: Chain C: D.65, D.67, D.70, D.102, K.104 Ligands: MG.22, MG.23, F.29, POP.30 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.65, C:D.70, C:D.102, H2O.16 MG.22: 6 residues within 4Å: Chain C: Y.55, D.67, D.70 Ligands: MG.21, F.29, POP.30 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.70, H2O.15, H2O.16, H2O.17 MG.23: 7 residues within 4Å: Chain C: D.65, D.97, D.102, K.104, K.142 Ligands: MG.21, POP.30 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.97, C:D.102, H2O.17, H2O.18 MG.24: 4 residues within 4Å: Chain C: K.29, E.31, D.67 Ligands: POP.30 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.31, H2O.18, H2O.22, H2O.22 MG.31: 9 residues within 4Å: Chain D: D.65, D.67, D.70, D.102, K.104 Ligands: MG.32, MG.33, F.39, POP.40 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.65, D:D.70, D:D.102, H2O.23 MG.32: 6 residues within 4Å: Chain D: Y.55, D.67, D.70 Ligands: MG.31, F.39, POP.40 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.70, H2O.23, H2O.23, H2O.24 MG.33: 7 residues within 4Å: Chain D: D.65, D.97, D.102, K.104, K.142 Ligands: MG.31, POP.40 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.97, D:D.102, H2O.25, H2O.25 MG.34: 4 residues within 4Å: Chain D: K.29, E.31, D.67 Ligands: POP.40 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.31, H2O.25, H2O.29, H2O.29 MG.41: 9 residues within 4Å: Chain E: D.65, D.67, D.70, D.102, K.104 Ligands: MG.42, MG.43, F.49, POP.50 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.65, E:D.70, E:D.102, H2O.31 MG.42: 6 residues within 4Å: Chain E: Y.55, D.67, D.70 Ligands: MG.41, F.49, POP.50 4 PLIP interactions: 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:D.70, H2O.30, H2O.30, H2O.32 MG.43: 7 residues within 4Å: Chain E: D.65, D.97, D.102, K.104, K.142 Ligands: MG.41, POP.50 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.97, E:D.102, H2O.32, H2O.32 MG.44: 4 residues within 4Å: Chain E: K.29, E.31, D.67 Ligands: POP.50 4 PLIP interactions: 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:E.31, H2O.33, H2O.37, H2O.37 MG.51: 9 residues within 4Å: Chain F: D.65, D.67, D.70, D.102, K.104 Ligands: MG.52, MG.53, F.59, POP.60 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.65, F:D.70, F:D.102, H2O.38 MG.52: 6 residues within 4Å: Chain F: Y.55, D.67, D.70 Ligands: MG.51, F.59, POP.60 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:D.70, H2O.37, H2O.38, H2O.39 MG.53: 7 residues within 4Å: Chain F: D.65, D.97, D.102, K.104, K.142 Ligands: MG.51, POP.60 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.97, F:D.102, H2O.39, H2O.39 MG.54: 4 residues within 4Å: Chain F: K.29, E.31, D.67 Ligands: POP.60 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:E.31, H2O.40, H2O.44, H2O.44

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

NA.5: 3 residues within 4Å: Chain A: K.142, E.145, K.148 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.145, A:E.145, A:K.148 NA.6: 2 residues within 4Å: Chain D: N.24 Ligands: NA.36 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.24 NA.15: 3 residues within 4Å: Chain B: K.142, E.145, K.148 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.145, B:E.145, B:K.148 NA.16: 2 residues within 4Å: Chain F: N.24 Ligands: NA.56 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.24 NA.25: 3 residues within 4Å: Chain C: K.142, E.145, K.148 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.145, C:E.145, C:K.148 NA.26: 2 residues within 4Å: Chain E: N.24 Ligands: NA.46 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.24 NA.35: 3 residues within 4Å: Chain D: K.142, E.145, K.148 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:E.145, D:E.145, D:K.148 NA.36: 2 residues within 4Å: Chain A: N.24 Ligands: NA.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.24 NA.45: 3 residues within 4Å: Chain E: K.142, E.145, K.148 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:E.145, E:E.145, E:K.148 NA.46: 2 residues within 4Å: Chain C: N.24 Ligands: NA.26 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.24 NA.55: 3 residues within 4Å: Chain F: K.142, E.145, K.148 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:E.145, F:E.145, F:K.148 NA.56: 2 residues within 4Å: Chain B: N.24 Ligands: NA.16 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.24

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

CL.7: 3 residues within 4Å: Chain A: P.6, A.7, G.8 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: K.131, A.132, W.155 Ligand excluded by PLIP CL.17: 3 residues within 4Å: Chain B: P.6, A.7, G.8 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain B: K.131, A.132, W.155 Ligand excluded by PLIP CL.27: 3 residues within 4Å: Chain C: P.6, A.7, G.8 Ligand excluded by PLIP CL.28: 3 residues within 4Å: Chain C: K.131, A.132, W.155 Ligand excluded by PLIP CL.37: 3 residues within 4Å: Chain D: P.6, A.7, G.8 Ligand excluded by PLIP CL.38: 3 residues within 4Å: Chain D: K.131, A.132, W.155 Ligand excluded by PLIP CL.47: 3 residues within 4Å: Chain E: P.6, A.7, G.8 Ligand excluded by PLIP CL.48: 3 residues within 4Å: Chain E: K.131, A.132, W.155 Ligand excluded by PLIP CL.57: 3 residues within 4Å: Chain F: P.6, A.7, G.8 Ligand excluded by PLIP CL.58: 3 residues within 4Å: Chain F: K.131, A.132, W.155 Ligand excluded by PLIP

6 x F: FLUORIDE ION(Non-covalent)

F.9: 7 residues within 4Å: Chain A: D.65, D.67, P.68, D.70 Ligands: MG.1, MG.2, POP.10 No protein-ligand interaction detected (PLIP) F.19: 7 residues within 4Å: Chain B: D.65, D.67, P.68, D.70 Ligands: MG.11, MG.12, POP.20 No protein-ligand interaction detected (PLIP) F.29: 7 residues within 4Å: Chain C: D.65, D.67, P.68, D.70 Ligands: MG.21, MG.22, POP.30 No protein-ligand interaction detected (PLIP) F.39: 7 residues within 4Å: Chain D: D.65, D.67, P.68, D.70 Ligands: MG.31, MG.32, POP.40 No protein-ligand interaction detected (PLIP) F.49: 7 residues within 4Å: Chain E: D.65, D.67, P.68, D.70 Ligands: MG.41, MG.42, POP.50 No protein-ligand interaction detected (PLIP) F.59: 7 residues within 4Å: Chain F: D.65, D.67, P.68, D.70 Ligands: MG.51, MG.52, POP.60 No protein-ligand interaction detected (PLIP)

6 x POP: PYROPHOSPHATE 2-(Non-covalent)

POP.10: 17 residues within 4Å: Chain A: K.29, E.31, R.43, Y.55, D.65, D.67, D.70, D.97, D.102, K.104, Y.141, K.142 Ligands: MG.1, MG.2, MG.3, MG.4, F.9 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:E.31, A:Y.55, A:D.67, A:Y.141 Water bridges: A:R.43, A:Y.51, A:K.104, A:K.104 Salt bridges: A:K.29, A:K.29, A:R.43, A:K.104, A:K.142 POP.20: 17 residues within 4Å: Chain B: K.29, E.31, R.43, Y.55, D.65, D.67, D.70, D.97, D.102, K.104, Y.141, K.142 Ligands: MG.11, MG.12, MG.13, MG.14, F.19 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:E.31, B:Y.55, B:Y.55, B:D.65, B:D.67, B:Y.141 Water bridges: B:E.31, B:E.31, B:Y.51, B:D.65, B:D.67, B:D.97, B:D.97 Salt bridges: B:K.29, B:K.29, B:R.43, B:K.104, B:K.142 POP.30: 17 residues within 4Å: Chain C: K.29, E.31, R.43, Y.55, D.65, D.67, D.70, D.97, D.102, K.104, Y.141, K.142 Ligands: MG.21, MG.22, MG.23, MG.24, F.29 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:E.31, C:Y.55, C:D.67, C:Y.141 Water bridges: C:R.43, C:Y.51, C:K.104, C:K.104 Salt bridges: C:K.29, C:K.29, C:R.43, C:K.104, C:K.142 POP.40: 17 residues within 4Å: Chain D: K.29, E.31, R.43, Y.55, D.65, D.67, D.70, D.97, D.102, K.104, Y.141, K.142 Ligands: MG.31, MG.32, MG.33, MG.34, F.39 8 PLIP interactions: 8 interactions with chain D Water bridges: D:R.43, D:Y.141, D:Y.141 Salt bridges: D:K.29, D:K.29, D:R.43, D:K.104, D:K.142 POP.50: 17 residues within 4Å: Chain E: K.29, E.31, R.43, Y.55, D.65, D.67, D.70, D.97, D.102, K.104, Y.141, K.142 Ligands: MG.41, MG.42, MG.43, MG.44, F.49 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:Y.55 Water bridges: E:E.31, E:E.31, E:D.65, E:D.67, E:Y.141, E:Y.141 Salt bridges: E:K.29, E:K.29, E:R.43, E:K.104, E:K.142 POP.60: 17 residues within 4Å: Chain F: K.29, E.31, R.43, Y.55, D.65, D.67, D.70, D.97, D.102, K.104, Y.141, K.142 Ligands: MG.51, MG.52, MG.53, MG.54, F.59 8 PLIP interactions: 8 interactions with chain F Water bridges: F:R.43, F:Y.141, F:Y.141 Salt bridges: F:K.29, F:K.29, F:R.43, F:K.104, F:K.142

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Samygina, V.R. et al., Reversible inhibition of Escherichia coli inorganic pyrophosphatase by fluoride: trapped catalytic intermediates in cryo-crystallographic studies. J.Mol.Biol. (2007)

Release Date

2006-08-29

Peptides

inorganic pyrophosphatase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

inorganic pyrophosphatase

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