SMTL ID : 2au7.1

The R43Q active site variant of E.coli inorganic pyrophosphatase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.05 Å

Oligo State

homo-hexamer

Ligands

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

PO4.1: 13 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.8 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.55 Water bridges: A:K.29, A:K.29, A:K.29 Salt bridges: A:K.29, A:K.104 PO4.12: 13 residues within 4Å: Chain B: K.29, E.31, Y.55, D.65, D.67, D.70, D.102, K.104 Ligands: MN.13, MN.14, MN.15, MN.16, CL.19 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.55 Water bridges: B:K.29, B:K.29, B:K.29 Salt bridges: B:K.29, B:K.104 PO4.23: 13 residues within 4Å: Chain C: K.29, E.31, Y.55, D.65, D.67, D.70, D.102, K.104 Ligands: MN.24, MN.25, MN.26, MN.27, CL.30 11 PLIP interactions: 11 interactions with chain C Hydrogen bonds: C:E.31, C:Y.55, C:D.65 Water bridges: C:K.29, C:K.29, C:K.29, C:Y.55, C:D.97, C:K.104 Salt bridges: C:K.29, C:K.104 PO4.34: 13 residues within 4Å: Chain D: K.29, E.31, Y.55, D.65, D.67, D.70, D.102, K.104 Ligands: MN.35, MN.36, MN.37, MN.38, CL.41 5 PLIP interactions: 5 interactions with chain D Water bridges: D:K.29, D:K.29, D:K.29 Salt bridges: D:K.29, D:K.104 PO4.45: 13 residues within 4Å: Chain E: K.29, E.31, Y.55, D.65, D.67, D.70, D.102, K.104 Ligands: MN.46, MN.47, MN.48, MN.49, CL.52 7 PLIP interactions: 7 interactions with chain E Water bridges: E:K.29, E:K.29, E:K.29, E:Y.55, E:K.104 Salt bridges: E:K.29, E:K.104 PO4.56: 13 residues within 4Å: Chain F: K.29, E.31, Y.55, D.65, D.67, D.70, D.102, K.104 Ligands: MN.57, MN.58, MN.59, MN.60, CL.63 5 PLIP interactions: 5 interactions with chain F Water bridges: F:K.29, F:K.29, F:K.29 Salt bridges: F:K.29, F:K.104

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

MN.2: 7 residues within 4Å: Chain A: D.65, D.70, D.102, K.104 Ligands: PO4.1, MN.3, MN.4 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: 4 residues within 4Å: Chain A: Y.55, D.70 Ligands: PO4.1, MN.2 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.70, H2O.1, H2O.1, H2O.2 MN.4: 6 residues within 4Å: Chain A: D.97, D.102, K.104 Ligands: PO4.1, MN.2, CL.8 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.97, A:D.102, H2O.3, H2O.5 MN.5: 5 residues within 4Å: Chain A: K.29, E.31, D.42, D.67 Ligands: PO4.1 6 PLIP interactions: 2 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.31, A:D.67, H2O.3, H2O.8, H2O.8, H2O.12 MN.6: 3 residues within 4Å: Chain A: A.25 Chain D: A.25 Ligands: MN.39 No protein-ligand interaction detected (PLIP) MN.13: 7 residues within 4Å: Chain B: D.65, D.70, D.102, K.104 Ligands: PO4.12, MN.14, MN.15 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.65, B:D.70, B:D.102, H2O.13 MN.14: 4 residues within 4Å: Chain B: Y.55, D.70 Ligands: PO4.12, MN.13 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.70, H2O.13, H2O.13, H2O.15 MN.15: 6 residues within 4Å: Chain B: D.97, D.102, K.104 Ligands: PO4.12, MN.13, CL.19 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.97, B:D.102, H2O.15, H2O.17 MN.16: 5 residues within 4Å: Chain B: K.29, E.31, D.42, D.67 Ligands: PO4.12 6 PLIP interactions: 2 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.31, B:D.67, H2O.16, H2O.20, H2O.20, H2O.24 MN.17: 3 residues within 4Å: Chain B: A.25 Chain F: A.25 Ligands: MN.61 No protein-ligand interaction detected (PLIP) MN.24: 7 residues within 4Å: Chain C: D.65, D.70, D.102, K.104 Ligands: PO4.23, MN.25, MN.26 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.65, C:D.70, C:D.102, H2O.26 MN.25: 4 residues within 4Å: Chain C: Y.55, D.70 Ligands: PO4.23, MN.24 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.70, H2O.25, H2O.25, H2O.27 MN.26: 6 residues within 4Å: Chain C: D.97, D.102, K.104 Ligands: PO4.23, MN.24, CL.30 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.97, C:D.102, H2O.27, H2O.29 MN.27: 5 residues within 4Å: Chain C: K.29, E.31, D.42, D.67 Ligands: PO4.23 6 PLIP interactions: 2 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:E.31, C:D.67, H2O.28, H2O.32, H2O.32, H2O.36 MN.28: 3 residues within 4Å: Chain C: A.25 Chain E: A.25 Ligands: MN.50 No protein-ligand interaction detected (PLIP) MN.35: 7 residues within 4Å: Chain D: D.65, D.70, D.102, K.104 Ligands: PO4.34, MN.36, MN.37 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.65, D:D.70, D:D.102, H2O.38 MN.36: 4 residues within 4Å: Chain D: Y.55, D.70 Ligands: PO4.34, MN.35 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.70, H2O.37, H2O.38, H2O.39 MN.37: 6 residues within 4Å: Chain D: D.97, D.102, K.104 Ligands: PO4.34, MN.35, CL.41 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.97, D:D.102, H2O.39, H2O.41 MN.38: 5 residues within 4Å: Chain D: K.29, E.31, D.42, D.67 Ligands: PO4.34 6 PLIP interactions: 2 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:E.31, D:D.67, H2O.40, H2O.45, H2O.45, H2O.48 MN.39: 3 residues within 4Å: Chain A: A.25 Chain D: A.25 Ligands: MN.6 No protein-ligand interaction detected (PLIP) MN.46: 7 residues within 4Å: Chain E: D.65, D.70, D.102, K.104 Ligands: PO4.45, MN.47, MN.48 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.65, E:D.70, E:D.102, H2O.50 MN.47: 4 residues within 4Å: Chain E: Y.55, D.70 Ligands: PO4.45, MN.46 4 PLIP interactions: 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:D.70, H2O.49, H2O.50, H2O.51 MN.48: 6 residues within 4Å: Chain E: D.97, D.102, K.104 Ligands: PO4.45, MN.46, CL.52 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.97, E:D.102, H2O.52, H2O.54 MN.49: 5 residues within 4Å: Chain E: K.29, E.31, D.42, D.67 Ligands: PO4.45 6 PLIP interactions: 2 interactions with chain E, 4 Ligand-Water interactions Metal complexes: E:E.31, E:D.67, H2O.52, H2O.57, H2O.57, H2O.61 MN.50: 3 residues within 4Å: Chain C: A.25 Chain E: A.25 Ligands: MN.28 No protein-ligand interaction detected (PLIP) MN.57: 7 residues within 4Å: Chain F: D.65, D.70, D.102, K.104 Ligands: PO4.56, MN.58, MN.59 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.65, F:D.70, F:D.102, H2O.62 MN.58: 4 residues within 4Å: Chain F: Y.55, D.70 Ligands: PO4.56, MN.57 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:D.70, H2O.62, H2O.62, H2O.63 MN.59: 6 residues within 4Å: Chain F: D.97, D.102, K.104 Ligands: PO4.56, MN.57, CL.63 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.97, F:D.102, H2O.64, H2O.66 MN.60: 5 residues within 4Å: Chain F: K.29, E.31, D.42, D.67 Ligands: PO4.56 6 PLIP interactions: 2 interactions with chain F, 4 Ligand-Water interactions Metal complexes: F:E.31, F:D.67, H2O.64, H2O.69, H2O.69, H2O.73 MN.61: 3 residues within 4Å: Chain B: A.25 Chain F: A.25 Ligands: MN.17 No protein-ligand interaction detected (PLIP)

6 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:D.143, A:E.145, A:K.148 NA.18: 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.29: 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.40: 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.51: 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.62: 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

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

CL.8: 8 residues within 4Å: Chain A: D.97, D.102, K.104, F.138, Y.141, K.142 Ligands: PO4.1, MN.4 Ligand excluded by PLIP CL.9: 4 residues within 4Å: Chain A: P.6, A.7, H.60, F.169 Ligand excluded by PLIP CL.10: 3 residues within 4Å: Chain A: K.131, A.132, W.155 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain A: R.88, H.110, S.111 Ligand excluded by PLIP CL.19: 8 residues within 4Å: Chain B: D.97, D.102, K.104, F.138, Y.141, K.142 Ligands: PO4.12, MN.15 Ligand excluded by PLIP CL.20: 4 residues within 4Å: Chain B: P.6, A.7, H.60, F.169 Ligand excluded by PLIP CL.21: 3 residues within 4Å: Chain B: K.131, A.132, W.155 Ligand excluded by PLIP CL.22: 3 residues within 4Å: Chain B: R.88, H.110, S.111 Ligand excluded by PLIP CL.30: 8 residues within 4Å: Chain C: D.97, D.102, K.104, F.138, Y.141, K.142 Ligands: PO4.23, MN.26 Ligand excluded by PLIP CL.31: 4 residues within 4Å: Chain C: P.6, A.7, H.60, F.169 Ligand excluded by PLIP CL.32: 3 residues within 4Å: Chain C: K.131, A.132, W.155 Ligand excluded by PLIP CL.33: 3 residues within 4Å: Chain C: R.88, H.110, S.111 Ligand excluded by PLIP CL.41: 8 residues within 4Å: Chain D: D.97, D.102, K.104, F.138, Y.141, K.142 Ligands: PO4.34, MN.37 Ligand excluded by PLIP CL.42: 4 residues within 4Å: Chain D: P.6, A.7, H.60, F.169 Ligand excluded by PLIP CL.43: 3 residues within 4Å: Chain D: K.131, A.132, W.155 Ligand excluded by PLIP CL.44: 3 residues within 4Å: Chain D: R.88, H.110, S.111 Ligand excluded by PLIP CL.52: 8 residues within 4Å: Chain E: D.97, D.102, K.104, F.138, Y.141, K.142 Ligands: PO4.45, MN.48 Ligand excluded by PLIP CL.53: 4 residues within 4Å: Chain E: P.6, A.7, H.60, F.169 Ligand excluded by PLIP CL.54: 3 residues within 4Å: Chain E: K.131, A.132, W.155 Ligand excluded by PLIP CL.55: 3 residues within 4Å: Chain E: R.88, H.110, S.111 Ligand excluded by PLIP CL.63: 8 residues within 4Å: Chain F: D.97, D.102, K.104, F.138, Y.141, K.142 Ligands: PO4.56, MN.59 Ligand excluded by PLIP CL.64: 4 residues within 4Å: Chain F: P.6, A.7, H.60, F.169 Ligand excluded by PLIP CL.65: 3 residues within 4Å: Chain F: K.131, A.132, W.155 Ligand excluded by PLIP CL.66: 3 residues within 4Å: Chain F: R.88, H.110, S.111 Ligand excluded by PLIP

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