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:D.143, 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:E.145, 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:E.145, F:K.148 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.21, H2O.155 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.23, H2O.161, H2O.197, H2O.1025 CA.4: 1 residues within 4Å: Chain A: D.70 5 PLIP interactions: 5 Ligand-Water interactions Metal complexes: H2O.13, H2O.68, H2O.199, H2O.200, H2O.230 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.38, H2O.194, H2O.222 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.74 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.277, H2O.297, H2O.431 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.299, H2O.437, H2O.473, H2O.1577 CA.13: 1 residues within 4Å: Chain B: D.70 5 PLIP interactions: 5 Ligand-Water interactions Metal complexes: H2O.289, H2O.344, H2O.475, H2O.476, H2O.506 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.314, H2O.470, H2O.498 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.350 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.553, H2O.573, H2O.707 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.575, H2O.713, H2O.749, H2O.1301 CA.22: 1 residues within 4Å: Chain C: D.70 5 PLIP interactions: 5 Ligand-Water interactions Metal complexes: H2O.565, H2O.620, H2O.751, H2O.752, H2O.782 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.590, H2O.746, H2O.774 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.626 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.829, H2O.849, H2O.983 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.197, H2O.851, H2O.989, H2O.1025 CA.31: 1 residues within 4Å: Chain D: D.70 5 PLIP interactions: 5 Ligand-Water interactions Metal complexes: H2O.841, H2O.896, H2O.1027, H2O.1028, H2O.1058 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.866, H2O.1022, H2O.1050 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.902 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.1105, H2O.1125, H2O.1259 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.749, H2O.1127, H2O.1265, H2O.1301 CA.40: 1 residues within 4Å: Chain E: D.70 5 PLIP interactions: 5 Ligand-Water interactions Metal complexes: H2O.1117, H2O.1172, H2O.1303, H2O.1304, H2O.1334 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.1142, H2O.1298, H2O.1326 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.1178 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.1381, H2O.1401, H2O.1535 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.473, H2O.1403, H2O.1541, H2O.1577 CA.49: 1 residues within 4Å: Chain F: D.70 5 PLIP interactions: 5 Ligand-Water interactions Metal complexes: H2O.1393, H2O.1448, H2O.1579, H2O.1580, H2O.1610 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.1418, H2O.1574, H2O.1602 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.1454

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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