- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.30 Å
- Oligo State
- homo-hexamer
- Ligands
- 30 x MN: MANGANESE (II) ION(Non-covalent)
- 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 PLIPCL.9: 4 residues within 4Å:- Chain A: P.6, A.7, H.60, F.169
Ligand excluded by PLIPCL.10: 3 residues within 4Å:- Chain A: K.131, A.132, W.155
Ligand excluded by PLIPCL.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 PLIPCL.21: 4 residues within 4Å:- Chain B: P.6, A.7, H.60, F.169
Ligand excluded by PLIPCL.22: 3 residues within 4Å:- Chain B: K.131, A.132, W.155
Ligand excluded by PLIPCL.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 PLIPCL.33: 4 residues within 4Å:- Chain C: P.6, A.7, H.60, F.169
Ligand excluded by PLIPCL.34: 3 residues within 4Å:- Chain C: K.131, A.132, W.155
Ligand excluded by PLIPCL.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 PLIPCL.45: 4 residues within 4Å:- Chain D: P.6, A.7, H.60, F.169
Ligand excluded by PLIPCL.46: 3 residues within 4Å:- Chain D: K.131, A.132, W.155
Ligand excluded by PLIPCL.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 PLIPCL.57: 4 residues within 4Å:- Chain E: P.6, A.7, H.60, F.169
Ligand excluded by PLIPCL.58: 3 residues within 4Å:- Chain E: K.131, A.132, W.155
Ligand excluded by PLIPCL.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 PLIPCL.69: 4 residues within 4Å:- Chain F: P.6, A.7, H.60, F.169
Ligand excluded by PLIPCL.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
AB
AC
AD
AE
AF
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.30 Å
- Oligo State
- homo-hexamer
- Ligands
- 30 x MN: MANGANESE (II) ION(Non-covalent)
- 12 x NA: SODIUM ION(Non-functional Binders)
- 18 x CL: CHLORIDE ION(Non-functional Binders)
- 6 x F: FLUORIDE ION(Non-covalent)
- 6 x POP: PYROPHOSPHATE 2-(Non-covalent)
- 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
AB
AC
AD
AE
AF
A