SMTL ID : 2au6.1

Crystal structure of catalytic intermediate of inorganic pyrophosphatase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

homo-hexamer

Ligands

6 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.1: 15 residues within 4Å: Chain A: K.29, E.31, Y.55, D.65, D.67, D.70, D.102, K.104 Ligands: MN.2, MN.3, MN.4, MN.5, CL.9, F.12, POP.13 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.55 Water bridges: A:K.29, A:K.29, A:Y.55 Salt bridges: A:K.29, A:K.104 PO4.14: 15 residues within 4Å: Chain B: K.29, E.31, Y.55, D.65, D.67, D.70, D.102, K.104 Ligands: MN.15, MN.16, MN.17, MN.18, CL.22, F.25, POP.26 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.55 Water bridges: B:K.29, B:K.29, B:Y.55 Salt bridges: B:K.29, B:K.104 PO4.27: 15 residues within 4Å: Chain C: K.29, E.31, Y.55, D.65, D.67, D.70, D.102, K.104 Ligands: MN.28, MN.29, MN.30, MN.31, CL.35, F.38, POP.39 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:Y.55 Water bridges: C:K.29, C:K.29, C:Y.55 Salt bridges: C:K.29, C:K.104 PO4.40: 15 residues within 4Å: Chain D: K.29, E.31, Y.55, D.65, D.67, D.70, D.102, K.104 Ligands: MN.41, MN.42, MN.43, MN.44, CL.48, F.51, POP.52 5 PLIP interactions: 5 interactions with chain D Water bridges: D:K.29, D:K.29, D:Y.55 Salt bridges: D:K.29, D:K.104 PO4.53: 15 residues within 4Å: Chain E: K.29, E.31, Y.55, D.65, D.67, D.70, D.102, K.104 Ligands: MN.54, MN.55, MN.56, MN.57, CL.61, F.64, POP.65 5 PLIP interactions: 5 interactions with chain E Water bridges: E:K.29, E:K.29, E:Y.55 Salt bridges: E:K.29, E:K.104 PO4.66: 15 residues within 4Å: Chain F: K.29, E.31, Y.55, D.65, D.67, D.70, D.102, K.104 Ligands: MN.67, MN.68, MN.69, MN.70, CL.74, F.77, POP.78 5 PLIP interactions: 5 interactions with chain F Water bridges: F:K.29, F:K.29, F:Y.55 Salt bridges: F:K.29, F:K.104

30 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 9 residues within 4Å: Chain A: D.65, D.70, D.102, K.104 Ligands: PO4.1, MN.3, MN.4, F.12, POP.13 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 MN.3: 6 residues within 4Å: Chain A: Y.55, D.70 Ligands: PO4.1, MN.2, F.12, POP.13 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.70, H2O.1, H2O.1, H2O.2, H2O.3 MN.4: 8 residues within 4Å: Chain A: D.65, D.97, D.102, K.104 Ligands: PO4.1, MN.2, CL.9, POP.13 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.97, A:D.102, H2O.3, H2O.9 MN.5: 6 residues within 4Å: Chain A: K.29, E.31, D.42, D.67 Ligands: PO4.1, POP.13 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.31, H2O.3, H2O.3, H2O.7, H2O.7 MN.6: 5 residues within 4Å: Chain A: N.24 Chain D: N.24 Ligands: NA.8, MN.45, NA.47 No protein-ligand interaction detected (PLIP) MN.15: 9 residues within 4Å: Chain B: D.65, D.70, D.102, K.104 Ligands: PO4.14, MN.16, MN.17, F.25, POP.26 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.65, B:D.70, B:D.102, H2O.12 MN.16: 6 residues within 4Å: Chain B: Y.55, D.70 Ligands: PO4.14, MN.15, F.25, POP.26 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.70, H2O.12, H2O.12, H2O.14, H2O.14 MN.17: 8 residues within 4Å: Chain B: D.65, D.97, D.102, K.104 Ligands: PO4.14, MN.15, CL.22, POP.26 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.97, B:D.102, H2O.14, H2O.20 MN.18: 6 residues within 4Å: Chain B: K.29, E.31, D.42, D.67 Ligands: PO4.14, POP.26 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.31, H2O.14, H2O.15, H2O.18, H2O.19 MN.19: 5 residues within 4Å: Chain B: N.24 Chain F: N.24 Ligands: NA.21, MN.71, NA.73 No protein-ligand interaction detected (PLIP) MN.28: 9 residues within 4Å: Chain C: D.65, D.70, D.102, K.104 Ligands: PO4.27, MN.29, MN.30, F.38, POP.39 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.65, C:D.70, C:D.102, H2O.24 MN.29: 6 residues within 4Å: Chain C: Y.55, D.70 Ligands: PO4.27, MN.28, F.38, POP.39 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:D.70, H2O.23, H2O.23, H2O.25, H2O.25 MN.30: 8 residues within 4Å: Chain C: D.65, D.97, D.102, K.104 Ligands: PO4.27, MN.28, CL.35, POP.39 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.97, C:D.102, H2O.25, H2O.31 MN.31: 6 residues within 4Å: Chain C: K.29, E.31, D.42, D.67 Ligands: PO4.27, POP.39 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:E.31, H2O.25, H2O.26, H2O.30, H2O.30 MN.32: 5 residues within 4Å: Chain C: N.24 Chain E: N.24 Ligands: NA.34, MN.58, NA.60 No protein-ligand interaction detected (PLIP) MN.41: 9 residues within 4Å: Chain D: D.65, D.70, D.102, K.104 Ligands: PO4.40, MN.42, MN.43, F.51, POP.52 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.65, D:D.70, D:D.102, H2O.35 MN.42: 6 residues within 4Å: Chain D: Y.55, D.70 Ligands: PO4.40, MN.41, F.51, POP.52 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:D.70, H2O.34, H2O.34, H2O.36, H2O.36 MN.43: 8 residues within 4Å: Chain D: D.65, D.97, D.102, K.104 Ligands: PO4.40, MN.41, CL.48, POP.52 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.97, D:D.102, H2O.36, H2O.42 MN.44: 6 residues within 4Å: Chain D: K.29, E.31, D.42, D.67 Ligands: PO4.40, POP.52 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:E.31, H2O.36, H2O.37, H2O.41, H2O.41 MN.45: 5 residues within 4Å: Chain A: N.24 Chain D: N.24 Ligands: MN.6, NA.8, NA.47 No protein-ligand interaction detected (PLIP) MN.54: 9 residues within 4Å: Chain E: D.65, D.70, D.102, K.104 Ligands: PO4.53, MN.55, MN.56, F.64, POP.65 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.65, E:D.70, E:D.102, H2O.46 MN.55: 6 residues within 4Å: Chain E: Y.55, D.70 Ligands: PO4.53, MN.54, F.64, POP.65 5 PLIP interactions: 1 interactions with chain E, 4 Ligand-Water interactions Metal complexes: E:D.70, H2O.45, H2O.46, H2O.47, H2O.47 MN.56: 8 residues within 4Å: Chain E: D.65, D.97, D.102, K.104 Ligands: PO4.53, MN.54, CL.61, POP.65 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.97, E:D.102, H2O.47, H2O.53 MN.57: 6 residues within 4Å: Chain E: K.29, E.31, D.42, D.67 Ligands: PO4.53, POP.65 5 PLIP interactions: 1 interactions with chain E, 4 Ligand-Water interactions Metal complexes: E:E.31, H2O.47, H2O.48, H2O.52, H2O.52 MN.58: 5 residues within 4Å: Chain C: N.24 Chain E: N.24 Ligands: MN.32, NA.34, NA.60 No protein-ligand interaction detected (PLIP) MN.67: 9 residues within 4Å: Chain F: D.65, D.70, D.102, K.104 Ligands: PO4.66, MN.68, MN.69, F.77, POP.78 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.65, F:D.70, F:D.102, H2O.57 MN.68: 6 residues within 4Å: Chain F: Y.55, D.70 Ligands: PO4.66, MN.67, F.77, POP.78 5 PLIP interactions: 1 interactions with chain F, 4 Ligand-Water interactions Metal complexes: F:D.70, H2O.56, H2O.57, H2O.58, H2O.58 MN.69: 8 residues within 4Å: Chain F: D.65, D.97, D.102, K.104 Ligands: PO4.66, MN.67, CL.74, POP.78 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.97, F:D.102, H2O.59, H2O.64 MN.70: 6 residues within 4Å: Chain F: K.29, E.31, D.42, D.67 Ligands: PO4.66, POP.78 5 PLIP interactions: 1 interactions with chain F, 4 Ligand-Water interactions Metal complexes: F:E.31, H2O.58, H2O.59, H2O.63, H2O.63 MN.71: 5 residues within 4Å: Chain B: N.24 Chain F: N.24 Ligands: MN.19, NA.21, NA.73 No protein-ligand interaction detected (PLIP)

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

NA.7: 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.8: 4 residues within 4Å: Chain D: N.24 Ligands: MN.6, MN.45, NA.47 No protein-ligand interaction detected (PLIP) NA.20: 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:K.148, B:K.148 NA.21: 4 residues within 4Å: Chain F: N.24 Ligands: MN.19, MN.71, NA.73 No protein-ligand interaction detected (PLIP) NA.33: 3 residues within 4Å: Chain C: K.142, E.145, K.148 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:K.142, C:E.145, C:K.148 NA.34: 4 residues within 4Å: Chain E: N.24 Ligands: MN.32, MN.58, NA.60 No protein-ligand interaction detected (PLIP) NA.46: 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:K.148, D:K.148 NA.47: 4 residues within 4Å: Chain A: N.24 Ligands: MN.6, NA.8, MN.45 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.24 NA.59: 3 residues within 4Å: Chain E: K.142, E.145, K.148 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:D.143, E:E.145, E:K.148 NA.60: 4 residues within 4Å: Chain C: N.24 Ligands: MN.32, NA.34, MN.58 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.24 NA.72: 3 residues within 4Å: Chain F: K.142, E.145, K.148 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:D.143, F:E.145, F:K.148 NA.73: 4 residues within 4Å: Chain B: N.24 Ligands: MN.19, NA.21, MN.71 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.24

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

CL.9: 8 residues within 4Å: Chain A: M.95, D.97, D.102, K.104, Y.141 Ligands: PO4.1, MN.4, POP.13 Ligand excluded by PLIP CL.10: 2 residues within 4Å: Chain A: A.7, G.8 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain A: K.131, A.132, W.155 Ligand excluded by PLIP CL.22: 8 residues within 4Å: Chain B: M.95, D.97, D.102, K.104, Y.141 Ligands: PO4.14, MN.17, POP.26 Ligand excluded by PLIP CL.23: 2 residues within 4Å: Chain B: A.7, G.8 Ligand excluded by PLIP CL.24: 3 residues within 4Å: Chain B: K.131, A.132, W.155 Ligand excluded by PLIP CL.35: 8 residues within 4Å: Chain C: M.95, D.97, D.102, K.104, Y.141 Ligands: PO4.27, MN.30, POP.39 Ligand excluded by PLIP CL.36: 2 residues within 4Å: Chain C: A.7, G.8 Ligand excluded by PLIP CL.37: 3 residues within 4Å: Chain C: K.131, A.132, W.155 Ligand excluded by PLIP CL.48: 8 residues within 4Å: Chain D: M.95, D.97, D.102, K.104, Y.141 Ligands: PO4.40, MN.43, POP.52 Ligand excluded by PLIP CL.49: 2 residues within 4Å: Chain D: A.7, G.8 Ligand excluded by PLIP CL.50: 3 residues within 4Å: Chain D: K.131, A.132, W.155 Ligand excluded by PLIP CL.61: 8 residues within 4Å: Chain E: M.95, D.97, D.102, K.104, Y.141 Ligands: PO4.53, MN.56, POP.65 Ligand excluded by PLIP CL.62: 2 residues within 4Å: Chain E: A.7, G.8 Ligand excluded by PLIP CL.63: 3 residues within 4Å: Chain E: K.131, A.132, W.155 Ligand excluded by PLIP CL.74: 8 residues within 4Å: Chain F: M.95, D.97, D.102, K.104, Y.141 Ligands: PO4.66, MN.69, POP.78 Ligand excluded by PLIP CL.75: 2 residues within 4Å: Chain F: A.7, G.8 Ligand excluded by PLIP CL.76: 3 residues within 4Å: Chain F: K.131, A.132, W.155 Ligand excluded by PLIP

6 x F: FLUORIDE ION(Non-covalent)

F.12: 7 residues within 4Å: Chain A: D.65, D.67, D.70 Ligands: PO4.1, MN.2, MN.3, POP.13 No protein-ligand interaction detected (PLIP) F.25: 7 residues within 4Å: Chain B: D.65, D.67, D.70 Ligands: PO4.14, MN.15, MN.16, POP.26 No protein-ligand interaction detected (PLIP) F.38: 7 residues within 4Å: Chain C: D.65, D.67, D.70 Ligands: PO4.27, MN.28, MN.29, POP.39 No protein-ligand interaction detected (PLIP) F.51: 7 residues within 4Å: Chain D: D.65, D.67, D.70 Ligands: PO4.40, MN.41, MN.42, POP.52 No protein-ligand interaction detected (PLIP) F.64: 7 residues within 4Å: Chain E: D.65, D.67, D.70 Ligands: PO4.53, MN.54, MN.55, POP.65 No protein-ligand interaction detected (PLIP) F.77: 7 residues within 4Å: Chain F: D.65, D.67, D.70 Ligands: PO4.66, MN.67, MN.68, POP.78 No protein-ligand interaction detected (PLIP)

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

POP.13: 20 residues within 4Å: Chain A: K.29, E.31, R.43, Y.51, Y.55, D.65, D.67, D.70, D.97, D.102, K.104, Y.141, K.142 Ligands: PO4.1, MN.2, MN.3, MN.4, MN.5, CL.9, F.12 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:Y.51, A:Y.55, A:Y.141 Water bridges: A:E.31, A:E.31, A:R.43, A:R.43, A:R.43, A:K.142, A:K.142, A:K.142 Salt bridges: A:K.29, A:K.29, A:R.43, A:K.104, A:K.142 POP.26: 20 residues within 4Å: Chain B: K.29, E.31, R.43, Y.51, Y.55, D.65, D.67, D.70, D.97, D.102, K.104, Y.141, K.142 Ligands: PO4.14, MN.15, MN.16, MN.17, MN.18, CL.22, F.25 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:Y.51, B:Y.55, B:Y.55, B:D.65, B:Y.141 Water bridges: B:E.31, B:E.31, B:E.31, B:R.43, B:R.43, B:D.65, B:D.102, B:K.142, B:K.142, B:K.142 Salt bridges: B:K.29, B:K.29, B:R.43, B:K.104, B:K.142 POP.39: 20 residues within 4Å: Chain C: K.29, E.31, R.43, Y.51, Y.55, D.65, D.67, D.70, D.97, D.102, K.104, Y.141, K.142 Ligands: PO4.27, MN.28, MN.29, MN.30, MN.31, CL.35, F.38 16 PLIP interactions: 16 interactions with chain C Hydrogen bonds: C:Y.51, C:Y.55, C:Y.141 Water bridges: C:E.31, C:E.31, C:R.43, C:R.43, C:R.43, C:K.142, C:K.142, C:K.142 Salt bridges: C:K.29, C:K.29, C:R.43, C:K.104, C:K.142 POP.52: 20 residues within 4Å: Chain D: K.29, E.31, R.43, Y.51, Y.55, D.65, D.67, D.70, D.97, D.102, K.104, Y.141, K.142 Ligands: PO4.40, MN.41, MN.42, MN.43, MN.44, CL.48, F.51 13 PLIP interactions: 13 interactions with chain D Water bridges: D:K.29, D:K.29, D:R.43, D:R.43, D:R.43, D:K.142, D:K.142, D:K.142 Salt bridges: D:K.29, D:K.29, D:R.43, D:K.104, D:K.142 POP.65: 20 residues within 4Å: Chain E: K.29, E.31, R.43, Y.51, Y.55, D.65, D.67, D.70, D.97, D.102, K.104, Y.141, K.142 Ligands: PO4.53, MN.54, MN.55, MN.56, MN.57, CL.61, F.64 17 PLIP interactions: 17 interactions with chain E Hydrogen bonds: E:Y.55 Water bridges: E:K.29, E:K.29, E:E.31, E:R.43, E:R.43, E:D.65, E:D.70, E:D.102, E:K.142, E:K.142, E:K.142 Salt bridges: E:K.29, E:K.29, E:R.43, E:K.104, E:K.142 POP.78: 20 residues within 4Å: Chain F: K.29, E.31, R.43, Y.51, Y.55, D.65, D.67, D.70, D.97, D.102, K.104, Y.141, K.142 Ligands: PO4.66, MN.67, MN.68, MN.69, MN.70, CL.74, F.77 13 PLIP interactions: 13 interactions with chain F Water bridges: F:K.29, F:K.29, F:R.43, F:R.43, F:R.43, F:K.142, F:K.142, F:K.142 Salt bridges: F:K.29, F:K.29, F:R.43, F:K.104, F:K.142

Links

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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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