SMTL ID : 2au9.1

Inorganic pyrophosphatase complexed with substrate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-hexamer

Ligands

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

MN.1: 7 residues within 4Å: Chain A: D.65, D.70, D.102 Ligands: MN.2, MN.3, F.11, POP.12 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.65, A:D.70, A:D.102, H2O.22 MN.2: 5 residues within 4Å: Chain A: Y.55, D.70 Ligands: MN.1, F.11, POP.12 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.70, H2O.8, H2O.15, H2O.53 MN.3: 7 residues within 4Å: Chain A: D.65, D.97, D.102, K.142 Ligands: MN.1, CL.8, POP.12 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.97, A:D.102, H2O.64 MN.4: 3 residues within 4Å: Chain A: E.31, D.67 Ligands: POP.12 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.31, H2O.78, H2O.179, H2O.180 MN.5: 3 residues within 4Å: Chain A: F.50 Chain D: A.25 Ligands: MN.41 No protein-ligand interaction detected (PLIP) MN.13: 7 residues within 4Å: Chain B: D.65, D.70, D.102 Ligands: MN.14, MN.15, F.23, POP.24 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.65, B:D.70, B:D.102, H2O.276 MN.14: 5 residues within 4Å: Chain B: Y.55, D.70 Ligands: MN.13, F.23, POP.24 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.70, H2O.262, H2O.269, H2O.307 MN.15: 7 residues within 4Å: Chain B: D.65, D.97, D.102, K.142 Ligands: MN.13, CL.20, POP.24 3 PLIP interactions: 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.97, B:D.102, H2O.318 MN.16: 3 residues within 4Å: Chain B: E.31, D.67 Ligands: POP.24 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:E.31, H2O.332, H2O.433, H2O.434 MN.17: 3 residues within 4Å: Chain B: F.50 Chain F: A.25 Ligands: MN.65 No protein-ligand interaction detected (PLIP) MN.25: 7 residues within 4Å: Chain C: D.65, D.70, D.102 Ligands: MN.26, MN.27, F.35, POP.36 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.65, C:D.70, C:D.102, H2O.530 MN.26: 5 residues within 4Å: Chain C: Y.55, D.70 Ligands: MN.25, F.35, POP.36 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.70, H2O.516, H2O.523, H2O.561 MN.27: 7 residues within 4Å: Chain C: D.65, D.97, D.102, K.142 Ligands: MN.25, CL.32, POP.36 3 PLIP interactions: 2 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.97, C:D.102, H2O.572 MN.28: 3 residues within 4Å: Chain C: E.31, D.67 Ligands: POP.36 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.31, H2O.586, H2O.687, H2O.688 MN.29: 3 residues within 4Å: Chain C: F.50 Chain E: A.25 Ligands: MN.53 No protein-ligand interaction detected (PLIP) MN.37: 7 residues within 4Å: Chain D: D.65, D.70, D.102 Ligands: MN.38, MN.39, F.47, POP.48 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.65, D:D.70, D:D.102, H2O.784 MN.38: 5 residues within 4Å: Chain D: Y.55, D.70 Ligands: MN.37, F.47, POP.48 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.70, H2O.770, H2O.777, H2O.815 MN.39: 7 residues within 4Å: Chain D: D.65, D.97, D.102, K.142 Ligands: MN.37, CL.44, POP.48 3 PLIP interactions: 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.97, D:D.102, H2O.826 MN.40: 3 residues within 4Å: Chain D: E.31, D.67 Ligands: POP.48 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:E.31, H2O.840, H2O.941, H2O.942 MN.41: 3 residues within 4Å: Chain A: A.25 Chain D: F.50 Ligands: MN.5 No protein-ligand interaction detected (PLIP) MN.49: 7 residues within 4Å: Chain E: D.65, D.70, D.102 Ligands: MN.50, MN.51, F.59, POP.60 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.65, E:D.70, E:D.102, H2O.1038 MN.50: 5 residues within 4Å: Chain E: Y.55, D.70 Ligands: MN.49, F.59, POP.60 4 PLIP interactions: 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:D.70, H2O.1024, H2O.1031, H2O.1069 MN.51: 7 residues within 4Å: Chain E: D.65, D.97, D.102, K.142 Ligands: MN.49, CL.56, POP.60 3 PLIP interactions: 2 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.97, E:D.102, H2O.1080 MN.52: 3 residues within 4Å: Chain E: E.31, D.67 Ligands: POP.60 4 PLIP interactions: 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:E.31, H2O.1094, H2O.1195, H2O.1196 MN.53: 3 residues within 4Å: Chain C: A.25 Chain E: F.50 Ligands: MN.29 No protein-ligand interaction detected (PLIP) MN.61: 7 residues within 4Å: Chain F: D.65, D.70, D.102 Ligands: MN.62, MN.63, F.71, POP.72 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.65, F:D.70, F:D.102, H2O.1292 MN.62: 5 residues within 4Å: Chain F: Y.55, D.70 Ligands: MN.61, F.71, POP.72 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:D.70, H2O.1278, H2O.1285, H2O.1323 MN.63: 7 residues within 4Å: Chain F: D.65, D.97, D.102, K.142 Ligands: MN.61, CL.68, POP.72 3 PLIP interactions: 2 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.97, F:D.102, H2O.1334 MN.64: 3 residues within 4Å: Chain F: E.31, D.67 Ligands: POP.72 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:E.31, H2O.1348, H2O.1449, H2O.1450 MN.65: 3 residues within 4Å: Chain B: A.25 Chain F: F.50 Ligands: MN.17 No protein-ligand interaction detected (PLIP)

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

NA.6: 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, A:K.148 NA.7: 2 residues within 4Å: Chain D: N.24 Ligands: NA.43 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.24 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:K.142, B:E.145, B:K.148 NA.19: 2 residues within 4Å: Chain F: N.24 Ligands: NA.67 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.24 NA.30: 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.31: 2 residues within 4Å: Chain E: N.24 Ligands: NA.55 No protein-ligand interaction detected (PLIP) NA.42: 3 residues within 4Å: Chain D: K.142, E.145, K.148 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.142, D:E.145, D:K.148 NA.43: 2 residues within 4Å: Chain A: N.24 Ligands: NA.7 No protein-ligand interaction detected (PLIP) NA.54: 3 residues within 4Å: Chain E: K.142, E.145, K.148 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:K.142, E:E.145, E:K.148 NA.55: 2 residues within 4Å: Chain C: N.24 Ligands: NA.31 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.24 NA.66: 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:E.145, F:K.148 NA.67: 2 residues within 4Å: Chain B: N.24 Ligands: NA.19 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.24

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

CL.8: 7 residues within 4Å: Chain A: M.95, D.97, D.102, K.104, Y.141 Ligands: MN.3, POP.12 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.20: 7 residues within 4Å: Chain B: M.95, D.97, D.102, K.104, Y.141 Ligands: MN.15, POP.24 Ligand excluded by PLIP CL.21: 4 residues within 4Å: Chain B: P.6, A.7, H.60, F.169 Ligand excluded by PLIP CL.22: 3 residues within 4Å: Chain B: K.131, A.132, W.155 Ligand excluded by PLIP CL.32: 7 residues within 4Å: Chain C: M.95, D.97, D.102, K.104, Y.141 Ligands: MN.27, POP.36 Ligand excluded by PLIP CL.33: 4 residues within 4Å: Chain C: P.6, A.7, H.60, F.169 Ligand excluded by PLIP CL.34: 3 residues within 4Å: Chain C: K.131, A.132, W.155 Ligand excluded by PLIP CL.44: 7 residues within 4Å: Chain D: M.95, D.97, D.102, K.104, Y.141 Ligands: MN.39, POP.48 Ligand excluded by PLIP CL.45: 4 residues within 4Å: Chain D: P.6, A.7, H.60, F.169 Ligand excluded by PLIP CL.46: 3 residues within 4Å: Chain D: K.131, A.132, W.155 Ligand excluded by PLIP CL.56: 7 residues within 4Å: Chain E: M.95, D.97, D.102, K.104, Y.141 Ligands: MN.51, POP.60 Ligand excluded by PLIP CL.57: 4 residues within 4Å: Chain E: P.6, A.7, H.60, F.169 Ligand excluded by PLIP CL.58: 3 residues within 4Å: Chain E: K.131, A.132, W.155 Ligand excluded by PLIP CL.68: 7 residues within 4Å: Chain F: M.95, D.97, D.102, K.104, Y.141 Ligands: MN.63, POP.72 Ligand excluded by PLIP CL.69: 4 residues within 4Å: Chain F: P.6, A.7, H.60, F.169 Ligand excluded by PLIP CL.70: 3 residues within 4Å: Chain F: K.131, A.132, W.155 Ligand excluded by PLIP

6 x F: FLUORIDE ION(Non-covalent)

F.11: 6 residues within 4Å: Chain A: D.65, D.67, D.70 Ligands: MN.1, MN.2, POP.12 No protein-ligand interaction detected (PLIP) F.23: 6 residues within 4Å: Chain B: D.65, D.67, D.70 Ligands: MN.13, MN.14, POP.24 No protein-ligand interaction detected (PLIP) F.35: 6 residues within 4Å: Chain C: D.65, D.67, D.70 Ligands: MN.25, MN.26, POP.36 No protein-ligand interaction detected (PLIP) F.47: 6 residues within 4Å: Chain D: D.65, D.67, D.70 Ligands: MN.37, MN.38, POP.48 No protein-ligand interaction detected (PLIP) F.59: 6 residues within 4Å: Chain E: D.65, D.67, D.70 Ligands: MN.49, MN.50, POP.60 No protein-ligand interaction detected (PLIP) F.71: 6 residues within 4Å: Chain F: D.65, D.67, D.70 Ligands: MN.61, MN.62, POP.72 No protein-ligand interaction detected (PLIP)

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

POP.12: 18 residues within 4Å: Chain A: K.29, E.31, R.43, Y.55, D.65, D.67, D.70, D.97, D.102, K.104, Y.141, K.142 Ligands: MN.1, MN.2, MN.3, MN.4, CL.8, F.11 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:Y.55, A:D.67, A:Y.141 Water bridges: A:K.29, A:K.29, A:Y.51, A:K.142, A:K.142 Salt bridges: A:K.29, A:K.29, A:R.43, A:K.104, A:K.142 POP.24: 18 residues within 4Å: Chain B: K.29, E.31, R.43, Y.55, D.65, D.67, D.70, D.97, D.102, K.104, Y.141, K.142 Ligands: MN.13, MN.14, MN.15, MN.16, CL.20, F.23 19 PLIP interactions: 19 interactions with chain B Hydrogen bonds: B:Y.55, B:Y.55, B:D.67, B:Y.141 Water bridges: B:K.29, B:K.29, B:E.31, B:E.31, B:Y.51, B:D.65, B:D.65, B:D.67, B:K.142, B:K.142 Salt bridges: B:K.29, B:K.29, B:R.43, B:K.104, B:K.142 POP.36: 18 residues within 4Å: Chain C: K.29, E.31, R.43, Y.55, D.65, D.67, D.70, D.97, D.102, K.104, Y.141, K.142 Ligands: MN.25, MN.26, MN.27, MN.28, CL.32, F.35 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:Y.55, C:D.67, C:Y.141 Water bridges: C:K.29, C:K.29, C:Y.51, C:K.142, C:K.142 Salt bridges: C:K.29, C:K.29, C:R.43, C:K.104, C:K.142 POP.48: 18 residues within 4Å: Chain D: K.29, E.31, R.43, Y.55, D.65, D.67, D.70, D.97, D.102, K.104, Y.141, K.142 Ligands: MN.37, MN.38, MN.39, MN.40, CL.44, F.47 13 PLIP interactions: 13 interactions with chain D Hydrogen bonds: D:Y.55 Water bridges: D:K.29, D:K.29, D:D.70, D:E.98, D:E.98, D:K.142, D:K.142 Salt bridges: D:K.29, D:K.29, D:R.43, D:K.104, D:K.142 POP.60: 18 residues within 4Å: Chain E: K.29, E.31, R.43, Y.55, D.65, D.67, D.70, D.97, D.102, K.104, Y.141, K.142 Ligands: MN.49, MN.50, MN.51, MN.52, CL.56, F.59 11 PLIP interactions: 11 interactions with chain E Water bridges: E:K.29, E:K.29, E:E.98, E:E.98, E:K.142, E:K.142 Salt bridges: E:K.29, E:K.29, E:R.43, E:K.104, E:K.142 POP.72: 18 residues within 4Å: Chain F: K.29, E.31, R.43, Y.55, D.65, D.67, D.70, D.97, D.102, K.104, Y.141, K.142 Ligands: MN.61, MN.62, MN.63, MN.64, CL.68, F.71 11 PLIP interactions: 11 interactions with chain F Water bridges: F:K.29, F:K.29, F:E.98, F:E.98, 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., 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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