SMTL ID : 1i6t.1

STRUCTURE OF INORGANIC PYROPHOSPHATASE

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.20 Å

Oligo State

homo-hexamer

Ligands

24 x CA: CALCIUM ION(Non-covalent)

CA.1: 6 residues within 4Å: Chain A: D.65, D.70, D.102 Ligands: CA.2, CA.3, POP.9 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.65, A:D.70, A:D.70, A:D.102, H2O.1 CA.2: 4 residues within 4Å: Chain A: Y.55, D.70 Ligands: CA.1, POP.9 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.70, H2O.1, H2O.1, H2O.1, H2O.1 CA.3: 5 residues within 4Å: Chain A: D.97, D.102, K.142 Ligands: CA.1, POP.9 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.97, A:D.102, H2O.3, H2O.5 CA.4: 2 residues within 4Å: Chain A: N.24 Ligands: CA.31 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:N.24, H2O.1, H2O.2, H2O.7, H2O.36 CA.10: 6 residues within 4Å: Chain B: D.65, D.70, D.102 Ligands: CA.11, CA.12, POP.18 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.65, B:D.70, B:D.70, B:D.102, H2O.11 CA.11: 4 residues within 4Å: Chain B: Y.55, D.70 Ligands: CA.10, POP.18 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.70, H2O.11, H2O.11, H2O.11, H2O.11 CA.12: 5 residues within 4Å: Chain B: D.97, D.102, K.142 Ligands: CA.10, POP.18 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.97, B:D.102, H2O.13, H2O.15 CA.13: 2 residues within 4Å: Chain B: N.24 Ligands: CA.49 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:N.24, H2O.11, H2O.11, H2O.16, H2O.56 CA.19: 6 residues within 4Å: Chain C: D.65, D.70, D.102 Ligands: CA.20, CA.21, POP.27 5 PLIP interactions: 4 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.65, C:D.70, C:D.70, C:D.102, H2O.21 CA.20: 4 residues within 4Å: Chain C: Y.55, D.70 Ligands: CA.19, POP.27 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:D.70, H2O.20, H2O.21, H2O.21, H2O.21 CA.21: 5 residues within 4Å: Chain C: D.97, D.102, K.142 Ligands: CA.19, POP.27 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.97, C:D.102, H2O.23, H2O.24 CA.22: 2 residues within 4Å: Chain C: N.24 Ligands: CA.40 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:N.24, H2O.20, H2O.21, H2O.26, H2O.46 CA.28: 6 residues within 4Å: Chain D: D.65, D.70, D.102 Ligands: CA.29, CA.30, POP.36 5 PLIP interactions: 4 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.65, D:D.70, D:D.70, D:D.102, H2O.31 CA.29: 4 residues within 4Å: Chain D: Y.55, D.70 Ligands: CA.28, POP.36 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:D.70, H2O.30, H2O.30, H2O.31, H2O.31 CA.30: 5 residues within 4Å: Chain D: D.97, D.102, K.142 Ligands: CA.28, POP.36 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.97, D:D.102, H2O.32, H2O.34 CA.31: 2 residues within 4Å: Chain D: N.24 Ligands: CA.4 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:N.24, H2O.7, H2O.30, H2O.31, H2O.36 CA.37: 6 residues within 4Å: Chain E: D.65, D.70, D.102 Ligands: CA.38, CA.39, POP.45 5 PLIP interactions: 4 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.65, E:D.70, E:D.70, E:D.102, H2O.41 CA.38: 4 residues within 4Å: Chain E: Y.55, D.70 Ligands: CA.37, POP.45 5 PLIP interactions: 1 interactions with chain E, 4 Ligand-Water interactions Metal complexes: E:D.70, H2O.40, H2O.40, H2O.40, H2O.41 CA.39: 5 residues within 4Å: Chain E: D.97, D.102, K.142 Ligands: CA.37, POP.45 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.97, E:D.102, H2O.42, H2O.44 CA.40: 2 residues within 4Å: Chain E: N.24 Ligands: CA.22 5 PLIP interactions: 1 interactions with chain E, 4 Ligand-Water interactions Metal complexes: E:N.24, H2O.26, H2O.40, H2O.41, H2O.46 CA.46: 6 residues within 4Å: Chain F: D.65, D.70, D.102 Ligands: CA.47, CA.48, POP.54 5 PLIP interactions: 4 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.65, F:D.70, F:D.70, F:D.102, H2O.50 CA.47: 4 residues within 4Å: Chain F: Y.55, D.70 Ligands: CA.46, POP.54 5 PLIP interactions: 1 interactions with chain F, 4 Ligand-Water interactions Metal complexes: F:D.70, H2O.50, H2O.50, H2O.50, H2O.50 CA.48: 5 residues within 4Å: Chain F: D.97, D.102, K.142 Ligands: CA.46, POP.54 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.97, F:D.102, H2O.52, H2O.54 CA.49: 2 residues within 4Å: Chain F: N.24 Ligands: CA.13 5 PLIP interactions: 1 interactions with chain F, 4 Ligand-Water interactions Metal complexes: F:N.24, H2O.16, H2O.50, H2O.50, H2O.56

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

NA.5: 3 residues within 4Å: Chain A: K.142, E.145, K.148 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.143, A:E.145, A:K.148 Water bridges: A:G.147 NA.14: 3 residues within 4Å: Chain B: K.142, E.145, K.148 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.143, B:E.145, B:K.148 Water bridges: B:G.147 NA.23: 3 residues within 4Å: Chain C: K.142, E.145, K.148 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:E.145, C:K.148, C:K.148 Water bridges: C:G.147 NA.32: 3 residues within 4Å: Chain D: K.142, E.145, K.148 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:E.145, D:K.148, D:K.148 Water bridges: D:G.147 NA.41: 3 residues within 4Å: Chain E: K.142, E.145, K.148 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:E.145, E:E.145, E:K.148 Water bridges: E:G.147 NA.50: 3 residues within 4Å: Chain F: K.142, E.145, K.148 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:D.143, F:E.145, F:K.148 Water bridges: F:G.147

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

CL.6: 3 residues within 4Å: Chain A: R.88, H.110, S.111 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain A: P.6, A.7, H.60, F.169 Ligand excluded by PLIP CL.8: 6 residues within 4Å: Chain A: A.23, C.53, N.54, V.73, P.74, T.75 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain B: R.88, H.110, S.111 Ligand excluded by PLIP CL.16: 4 residues within 4Å: Chain B: P.6, A.7, H.60, F.169 Ligand excluded by PLIP CL.17: 6 residues within 4Å: Chain B: A.23, C.53, N.54, V.73, P.74, T.75 Ligand excluded by PLIP CL.24: 3 residues within 4Å: Chain C: R.88, H.110, S.111 Ligand excluded by PLIP CL.25: 4 residues within 4Å: Chain C: P.6, A.7, H.60, F.169 Ligand excluded by PLIP CL.26: 6 residues within 4Å: Chain C: A.23, C.53, N.54, V.73, P.74, T.75 Ligand excluded by PLIP CL.33: 3 residues within 4Å: Chain D: R.88, H.110, S.111 Ligand excluded by PLIP CL.34: 4 residues within 4Å: Chain D: P.6, A.7, H.60, F.169 Ligand excluded by PLIP CL.35: 6 residues within 4Å: Chain D: A.23, C.53, N.54, V.73, P.74, T.75 Ligand excluded by PLIP CL.42: 3 residues within 4Å: Chain E: R.88, H.110, S.111 Ligand excluded by PLIP CL.43: 4 residues within 4Å: Chain E: P.6, A.7, H.60, F.169 Ligand excluded by PLIP CL.44: 6 residues within 4Å: Chain E: A.23, C.53, N.54, V.73, P.74, T.75 Ligand excluded by PLIP CL.51: 3 residues within 4Å: Chain F: R.88, H.110, S.111 Ligand excluded by PLIP CL.52: 4 residues within 4Å: Chain F: P.6, A.7, H.60, F.169 Ligand excluded by PLIP CL.53: 6 residues within 4Å: Chain F: A.23, C.53, N.54, V.73, P.74, T.75 Ligand excluded by PLIP

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

POP.9: 13 residues within 4Å: Chain A: K.29, R.43, Y.55, D.65, D.70, D.97, D.102, K.104, Y.141, K.142 Ligands: CA.1, CA.2, CA.3 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:E.31, A:Y.55, A:Y.55, A:D.70, A:Y.141 Water bridges: A:K.29, A:K.29, A:K.29, A:K.29, A:K.29, A:D.102, A:K.142, A:K.142 Salt bridges: A:K.29, A:K.29, A:R.43, A:K.104, A:K.142 POP.18: 13 residues within 4Å: Chain B: K.29, R.43, Y.55, D.65, D.70, D.97, D.102, K.104, Y.141, K.142 Ligands: CA.10, CA.11, CA.12 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:E.31, B:Y.55, B:Y.55, B:D.70, B:Y.141 Water bridges: B:K.29, B:K.29, B:K.29, B:K.29, B:K.29, B:D.102, B:K.142, B:K.142 Salt bridges: B:K.29, B:K.29, B:R.43, B:K.104, B:K.142 POP.27: 13 residues within 4Å: Chain C: K.29, R.43, Y.55, D.65, D.70, D.97, D.102, K.104, Y.141, K.142 Ligands: CA.19, CA.20, CA.21 21 PLIP interactions: 21 interactions with chain C Hydrogen bonds: C:E.31, C:Y.55, C:D.65, C:D.70, C:D.70, C:D.97, C:Y.141, C:Y.141 Water bridges: C:K.29, C:K.29, C:K.29, C:K.29, C:K.29, C:D.102, C:K.142, C:K.142 Salt bridges: C:K.29, C:K.29, C:R.43, C:K.104, C:K.142 POP.36: 13 residues within 4Å: Chain D: K.29, R.43, Y.55, D.65, D.70, D.97, D.102, K.104, Y.141, K.142 Ligands: CA.28, CA.29, CA.30 16 PLIP interactions: 16 interactions with chain D Hydrogen bonds: D:Y.55, D:D.70 Water bridges: D:K.29, D:K.29, D:K.29, D:K.29, D:K.29, D:Y.141, 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.45: 13 residues within 4Å: Chain E: K.29, R.43, Y.55, D.65, D.70, D.97, D.102, K.104, Y.141, K.142 Ligands: CA.37, CA.38, CA.39 16 PLIP interactions: 16 interactions with chain E Hydrogen bonds: E:Y.55, E:D.70 Water bridges: E:K.29, E:K.29, E:K.29, E:K.29, E:K.29, E:Y.141, 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.54: 13 residues within 4Å: Chain F: K.29, R.43, Y.55, D.65, D.70, D.97, D.102, K.104, Y.141, K.142 Ligands: CA.46, CA.47, CA.48 16 PLIP interactions: 16 interactions with chain F Hydrogen bonds: F:Y.55, F:D.70 Water bridges: F:K.29, F:K.29, F:K.29, F:K.29, F:K.29, F:Y.141, 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

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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