SMTL ID : 2au8.1

Catalytic intermediate structure of inorganic pyrophosphatase

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-hexamer

Ligands

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

PO4.1: 12 residues within 4Å: Chain A: K.29, E.31, Y.55, D.65, D.70, D.102, K.104 Ligands: MN.2, MN.3, MN.4, MN.5, CL.8 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.55 Water bridges: A:R.43 Salt bridges: A:K.29, A:K.104 PO4.10: 12 residues within 4Å: Chain B: K.29, E.31, Y.55, D.65, D.70, D.102, K.104 Ligands: MN.11, MN.12, MN.13, MN.14, CL.17 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.55 Water bridges: B:R.43 Salt bridges: B:K.29, B:K.104 PO4.19: 12 residues within 4Å: Chain C: K.29, E.31, Y.55, D.65, D.70, D.102, K.104 Ligands: MN.20, MN.21, MN.22, MN.23, CL.26 6 PLIP interactions: 6 interactions with chain C Hydrogen bonds: C:Y.55 Water bridges: C:E.31, C:E.31, C:R.43 Salt bridges: C:K.29, C:K.104 PO4.28: 12 residues within 4Å: Chain D: K.29, E.31, Y.55, D.65, D.70, D.102, K.104 Ligands: MN.29, MN.30, MN.31, MN.32, CL.35 3 PLIP interactions: 3 interactions with chain D Water bridges: D:R.43 Salt bridges: D:K.29, D:K.104 PO4.37: 12 residues within 4Å: Chain E: K.29, E.31, Y.55, D.65, D.70, D.102, K.104 Ligands: MN.38, MN.39, MN.40, MN.41, CL.44 3 PLIP interactions: 3 interactions with chain E Water bridges: E:R.43 Salt bridges: E:K.29, E:K.104 PO4.46: 12 residues within 4Å: Chain F: K.29, E.31, Y.55, D.65, D.70, D.102, K.104 Ligands: MN.47, MN.48, MN.49, MN.50, CL.53 3 PLIP interactions: 3 interactions with chain F Water bridges: F:R.43 Salt bridges: F:K.29, F:K.104

24 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.22 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.8, H2O.15, H2O.52 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.64, H2O.116 MN.5: 2 residues within 4Å: Chain A: E.31 Ligands: PO4.1 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:E.31, H2O.56, H2O.58, H2O.77, H2O.78 MN.11: 7 residues within 4Å: Chain B: D.65, D.70, D.102, K.104 Ligands: PO4.10, MN.12, MN.13 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.65, B:D.70, B:D.102, H2O.152 MN.12: 4 residues within 4Å: Chain B: Y.55, D.70 Ligands: PO4.10, MN.11 4 PLIP interactions: 1 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.70, H2O.138, H2O.145, H2O.182 MN.13: 6 residues within 4Å: Chain B: D.97, D.102, K.104 Ligands: PO4.10, MN.11, CL.17 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.97, B:D.102, H2O.194, H2O.246 MN.14: 2 residues within 4Å: Chain B: E.31 Ligands: PO4.10 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.31, H2O.186, H2O.188, H2O.207, H2O.208 MN.20: 7 residues within 4Å: Chain C: D.65, D.70, D.102, K.104 Ligands: PO4.19, MN.21, MN.22 4 PLIP interactions: 3 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.65, C:D.70, C:D.102, H2O.282 MN.21: 4 residues within 4Å: Chain C: Y.55, D.70 Ligands: PO4.19, MN.20 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:D.70, H2O.268, H2O.275, H2O.312 MN.22: 6 residues within 4Å: Chain C: D.97, D.102, K.104 Ligands: PO4.19, MN.20, CL.26 4 PLIP interactions: 2 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.97, C:D.102, H2O.324, H2O.376 MN.23: 2 residues within 4Å: Chain C: E.31 Ligands: PO4.19 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:E.31, H2O.316, H2O.318, H2O.337, H2O.338 MN.29: 7 residues within 4Å: Chain D: D.65, D.70, D.102, K.104 Ligands: PO4.28, MN.30, MN.31 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.65, D:D.70, D:D.102, H2O.412 MN.30: 4 residues within 4Å: Chain D: Y.55, D.70 Ligands: PO4.28, MN.29 4 PLIP interactions: 1 interactions with chain D, 3 Ligand-Water interactions Metal complexes: D:D.70, H2O.398, H2O.405, H2O.442 MN.31: 6 residues within 4Å: Chain D: D.97, D.102, K.104 Ligands: PO4.28, MN.29, CL.35 4 PLIP interactions: 2 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.97, D:D.102, H2O.454, H2O.506 MN.32: 2 residues within 4Å: Chain D: E.31 Ligands: PO4.28 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:E.31, H2O.446, H2O.448, H2O.467, H2O.468 MN.38: 7 residues within 4Å: Chain E: D.65, D.70, D.102, K.104 Ligands: PO4.37, MN.39, MN.40 4 PLIP interactions: 3 interactions with chain E, 1 Ligand-Water interactions Metal complexes: E:D.65, E:D.70, E:D.102, H2O.542 MN.39: 4 residues within 4Å: Chain E: Y.55, D.70 Ligands: PO4.37, MN.38 4 PLIP interactions: 1 interactions with chain E, 3 Ligand-Water interactions Metal complexes: E:D.70, H2O.528, H2O.535, H2O.572 MN.40: 6 residues within 4Å: Chain E: D.97, D.102, K.104 Ligands: PO4.37, MN.38, CL.44 4 PLIP interactions: 2 interactions with chain E, 2 Ligand-Water interactions Metal complexes: E:D.97, E:D.102, H2O.584, H2O.636 MN.41: 2 residues within 4Å: Chain E: E.31 Ligands: PO4.37 5 PLIP interactions: 1 interactions with chain E, 4 Ligand-Water interactions Metal complexes: E:E.31, H2O.576, H2O.578, H2O.597, H2O.598 MN.47: 7 residues within 4Å: Chain F: D.65, D.70, D.102, K.104 Ligands: PO4.46, MN.48, MN.49 4 PLIP interactions: 3 interactions with chain F, 1 Ligand-Water interactions Metal complexes: F:D.65, F:D.70, F:D.102, H2O.672 MN.48: 4 residues within 4Å: Chain F: Y.55, D.70 Ligands: PO4.46, MN.47 4 PLIP interactions: 1 interactions with chain F, 3 Ligand-Water interactions Metal complexes: F:D.70, H2O.658, H2O.665, H2O.702 MN.49: 6 residues within 4Å: Chain F: D.97, D.102, K.104 Ligands: PO4.46, MN.47, CL.53 4 PLIP interactions: 2 interactions with chain F, 2 Ligand-Water interactions Metal complexes: F:D.97, F:D.102, H2O.714, H2O.766 MN.50: 2 residues within 4Å: Chain F: E.31 Ligands: PO4.46 5 PLIP interactions: 1 interactions with chain F, 4 Ligand-Water interactions Metal complexes: F:E.31, H2O.706, H2O.708, H2O.727, H2O.728

6 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:E.145, A:E.145, A:K.148 NA.15: 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, B:K.148 NA.24: 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:K.148, C:K.148 NA.33: 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, D:K.148 NA.42: 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, E:K.148 NA.51: 3 residues within 4Å: Chain F: K.142, E.145, K.148 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:K.142, F:E.145, F:K.148

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

CL.7: 4 residues within 4Å: Chain A: P.6, A.7, H.60, F.169 Ligand excluded by PLIP CL.8: 7 residues within 4Å: Chain A: M.95, D.97, D.102, K.104, Y.141 Ligands: PO4.1, MN.4 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain A: K.131, A.132, W.155 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: 7 residues within 4Å: Chain B: M.95, D.97, D.102, K.104, Y.141 Ligands: PO4.10, MN.13 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain B: K.131, A.132, W.155 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: 7 residues within 4Å: Chain C: M.95, D.97, D.102, K.104, Y.141 Ligands: PO4.19, MN.22 Ligand excluded by PLIP CL.27: 3 residues within 4Å: Chain C: K.131, A.132, W.155 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: 7 residues within 4Å: Chain D: M.95, D.97, D.102, K.104, Y.141 Ligands: PO4.28, MN.31 Ligand excluded by PLIP CL.36: 3 residues within 4Å: Chain D: K.131, A.132, W.155 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: 7 residues within 4Å: Chain E: M.95, D.97, D.102, K.104, Y.141 Ligands: PO4.37, MN.40 Ligand excluded by PLIP CL.45: 3 residues within 4Å: Chain E: K.131, A.132, W.155 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: 7 residues within 4Å: Chain F: M.95, D.97, D.102, K.104, Y.141 Ligands: PO4.46, MN.49 Ligand excluded by PLIP CL.54: 3 residues within 4Å: Chain F: K.131, A.132, W.155 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

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