SMTL ID : 1i40.1

STRUCTURE OF INORGANIC PYROPHOSPHATASE

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.10 Å

Oligo State

homo-hexamer

Ligands

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

NA.1: 3 residues within 4Å: Chain A: K.142, E.145, K.148 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.142, A:E.145 Water bridges: A:K.148 NA.10: 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 Water bridges: B:K.148 NA.19: 3 residues within 4Å: Chain C: K.142, E.145, K.148 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:D.143, C:E.145 Water bridges: C:K.148 NA.28: 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 Water bridges: D:K.148 NA.37: 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 Water bridges: E:K.148 NA.46: 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 Water bridges: F:K.148

30 x CA: CALCIUM ION(Non-covalent)

CA.2: 3 residues within 4Å: Chain A: D.65, D.70, D.102 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.65, A:D.102, H2O.1, H2O.1, H2O.6 CA.3: 2 residues within 4Å: Chain A: N.24 Ligands: CA.30 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:N.24, H2O.1, H2O.7, H2O.8, H2O.40 CA.4: 1 residues within 4Å: Chain A: D.70 5 PLIP interactions: 5 Ligand-Water interactions Metal complexes: H2O.1, H2O.3, H2O.8, H2O.8, H2O.9 CA.5: 3 residues within 4Å: Chain A: E.139, V.150, K.151 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.139, A:V.150, H2O.2, H2O.8, H2O.9 CA.6: 2 residues within 4Å: Chain A: D.97, D.102 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.97, A:D.102, H2O.3 CA.11: 3 residues within 4Å: Chain B: D.65, D.70, D.102 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.65, B:D.102, H2O.11, H2O.12, H2O.17 CA.12: 2 residues within 4Å: Chain B: N.24 Ligands: CA.48 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:N.24, H2O.12, H2O.17, H2O.19, H2O.61 CA.13: 1 residues within 4Å: Chain B: D.70 5 PLIP interactions: 5 Ligand-Water interactions Metal complexes: H2O.12, H2O.14, H2O.19, H2O.19, H2O.20 CA.14: 3 residues within 4Å: Chain B: E.139, V.150, K.151 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.139, B:V.150, H2O.13, H2O.19, H2O.20 CA.15: 2 residues within 4Å: Chain B: D.97, D.102 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.97, B:D.102, H2O.14 CA.20: 3 residues within 4Å: Chain C: D.65, D.70, D.102 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.65, C:D.102, H2O.22, H2O.23, H2O.28 CA.21: 2 residues within 4Å: Chain C: N.24 Ligands: CA.39 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:N.24, H2O.23, H2O.28, H2O.29, H2O.51 CA.22: 1 residues within 4Å: Chain C: D.70 5 PLIP interactions: 5 Ligand-Water interactions Metal complexes: H2O.22, H2O.24, H2O.29, H2O.29, H2O.31 CA.23: 3 residues within 4Å: Chain C: E.139, V.150, K.151 5 PLIP interactions: 2 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.139, C:V.150, H2O.23, H2O.29, H2O.30 CA.24: 2 residues within 4Å: Chain C: D.97, D.102 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.97, C:D.102, H2O.25 CA.29: 3 residues within 4Å: Chain D: D.65, D.70, D.102 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.65, D:D.102, H2O.32, H2O.33, H2O.38 CA.30: 2 residues within 4Å: Chain D: N.24 Ligands: CA.3 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:N.24, H2O.8, H2O.33, H2O.39, H2O.40 CA.31: 1 residues within 4Å: Chain D: D.70 5 PLIP interactions: 5 Ligand-Water interactions Metal complexes: H2O.33, H2O.35, H2O.40, H2O.40, H2O.41 CA.32: 3 residues within 4Å: Chain D: E.139, V.150, K.151 5 PLIP interactions: 2 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.139, D:V.150, H2O.34, H2O.40, H2O.41 CA.33: 2 residues within 4Å: Chain D: D.97, D.102 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.97, D:D.102, H2O.35 CA.38: 3 residues within 4Å: Chain E: D.65, D.70, D.102 5 PLIP interactions: 2 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:D.65, E:D.102, H2O.43, H2O.44, H2O.49 CA.39: 2 residues within 4Å: Chain E: N.24 Ligands: CA.21 5 PLIP interactions: 1 interactions with chain E, 4 Ligand-Water interactions Metal complexes: E:N.24, H2O.29, H2O.44, H2O.49, H2O.51 CA.40: 1 residues within 4Å: Chain E: D.70 5 PLIP interactions: 5 Ligand-Water interactions Metal complexes: H2O.43, H2O.46, H2O.51, H2O.51, H2O.52 CA.41: 3 residues within 4Å: Chain E: E.139, V.150, K.151 5 PLIP interactions: 2 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:E.139, E:V.150, H2O.44, H2O.50, H2O.51 CA.42: 2 residues within 4Å: Chain E: D.97, D.102 3 PLIP interactions: 2 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.97, E:D.102, H2O.46 CA.47: 3 residues within 4Å: Chain F: D.65, D.70, D.102 5 PLIP interactions: 2 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:D.65, F:D.102, H2O.54, H2O.54, H2O.60 CA.48: 2 residues within 4Å: Chain F: N.24 Ligands: CA.12 5 PLIP interactions: 1 interactions with chain F, 4 Ligand-Water interactions Metal complexes: F:N.24, H2O.19, H2O.54, H2O.60, H2O.61 CA.49: 1 residues within 4Å: Chain F: D.70 5 PLIP interactions: 5 Ligand-Water interactions Metal complexes: H2O.54, H2O.56, H2O.61, H2O.61, H2O.62 CA.50: 3 residues within 4Å: Chain F: E.139, V.150, K.151 5 PLIP interactions: 2 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:E.139, F:V.150, H2O.55, H2O.61, H2O.62 CA.51: 2 residues within 4Å: Chain F: D.97, D.102 3 PLIP interactions: 2 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.97, F:D.102, H2O.56

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

CL.7: 3 residues within 4Å: Chain A: R.88, H.110, S.111 Ligand excluded by PLIP CL.8: 4 residues within 4Å: Chain A: P.6, A.7, H.60, F.169 Ligand excluded by PLIP CL.9: 5 residues within 4Å: Chain A: A.23, C.53, N.54, P.74, T.75 Ligand excluded by PLIP CL.16: 3 residues within 4Å: Chain B: R.88, H.110, S.111 Ligand excluded by PLIP CL.17: 4 residues within 4Å: Chain B: P.6, A.7, H.60, F.169 Ligand excluded by PLIP CL.18: 5 residues within 4Å: Chain B: A.23, C.53, N.54, P.74, T.75 Ligand excluded by PLIP CL.25: 3 residues within 4Å: Chain C: R.88, H.110, S.111 Ligand excluded by PLIP CL.26: 4 residues within 4Å: Chain C: P.6, A.7, H.60, F.169 Ligand excluded by PLIP CL.27: 5 residues within 4Å: Chain C: A.23, C.53, N.54, P.74, T.75 Ligand excluded by PLIP CL.34: 3 residues within 4Å: Chain D: R.88, H.110, S.111 Ligand excluded by PLIP CL.35: 4 residues within 4Å: Chain D: P.6, A.7, H.60, F.169 Ligand excluded by PLIP CL.36: 5 residues within 4Å: Chain D: A.23, C.53, N.54, P.74, T.75 Ligand excluded by PLIP CL.43: 3 residues within 4Å: Chain E: R.88, H.110, S.111 Ligand excluded by PLIP CL.44: 4 residues within 4Å: Chain E: P.6, A.7, H.60, F.169 Ligand excluded by PLIP CL.45: 5 residues within 4Å: Chain E: A.23, C.53, N.54, P.74, T.75 Ligand excluded by PLIP CL.52: 3 residues within 4Å: Chain F: R.88, H.110, S.111 Ligand excluded by PLIP CL.53: 4 residues within 4Å: Chain F: P.6, A.7, H.60, F.169 Ligand excluded by PLIP CL.54: 5 residues within 4Å: Chain F: A.23, C.53, N.54, P.74, T.75 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Samygina, V.R. et al., The structures of Escherichia coli inorganic pyrophosphatase complexed with Ca(2+) or CaPP(i) at atomic resolution and their mechanistic implications. J.Mol.Biol. (2001)

Release Date

2001-12-05

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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