SMTL ID : 3eiy.1 (2 other biounits)

Crystal structure of inorganic pyrophosphatase from burkholderia pseudomallei with bound pyrophosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-hexamer

Ligands

6 x K: POTASSIUM ION(Non-covalent)

K.1: 3 residues within 4Å: Chain A: D.32, L.33, Q.35 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.32, A:L.33 K.8: 3 residues within 4Å: Chain B: D.32, L.33, Q.35 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.32, B:L.33 K.15: 3 residues within 4Å: Chain C: D.32, L.33, Q.35 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.32, C:L.33 K.22: 3 residues within 4Å: Chain D: D.32, L.33, Q.35 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.32, D:L.33 K.29: 3 residues within 4Å: Chain E: D.32, L.33, Q.35 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.32, E:L.33 K.36: 3 residues within 4Å: Chain F: D.32, L.33, Q.35 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.32, F:L.33

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

NA.2: 5 residues within 4Å: Chain A: D.119, D.124, K.126, K.164 Ligands: POP.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.119, A:D.119, A:K.126, A:K.164 NA.3: 4 residues within 4Å: Chain A: D.87, D.92, D.124, A.125 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.92, A:D.124, A:A.125 Water bridges: A:S.85, A:D.92 NA.9: 5 residues within 4Å: Chain B: D.119, D.124, K.126, K.164 Ligands: POP.11 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.119, B:D.119, B:K.126, B:K.164 NA.10: 4 residues within 4Å: Chain B: D.87, D.92, D.124, A.125 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:D.92, B:A.125, B:A.125 Water bridges: B:S.85, B:S.85, B:D.92 NA.16: 5 residues within 4Å: Chain C: D.119, D.124, K.126, K.164 Ligands: POP.18 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:D.119, C:D.119, C:K.126, C:K.164 NA.17: 4 residues within 4Å: Chain C: D.87, D.92, D.124, A.125 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:D.92, C:D.124, C:A.125 Water bridges: C:S.85, C:D.92 NA.23: 5 residues within 4Å: Chain D: D.119, D.124, K.126, K.164 Ligands: POP.25 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.126, D:K.164, D:K.164 NA.24: 4 residues within 4Å: Chain D: D.87, D.92, D.124, A.125 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:D.92, D:D.124, D:A.125 Water bridges: D:S.85, D:D.92 NA.30: 5 residues within 4Å: Chain E: D.119, D.124, K.126, K.164 Ligands: POP.32 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:K.126, E:K.164, E:K.164 NA.31: 4 residues within 4Å: Chain E: D.87, D.92, D.124, A.125 5 PLIP interactions: 5 interactions with chain E Hydrogen bonds: E:D.87, E:D.124, E:A.125 Water bridges: E:S.85, E:D.92 NA.37: 5 residues within 4Å: Chain F: D.119, D.124, K.126, K.164 Ligands: POP.39 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:K.126, F:K.126, F:K.164 NA.38: 4 residues within 4Å: Chain F: D.87, D.92, D.124, A.125 6 PLIP interactions: 6 interactions with chain F Hydrogen bonds: F:D.87, F:D.124, F:A.125 Water bridges: F:S.85, F:S.85, F:D.92

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

POP.4: 9 residues within 4Å: Chain A: K.51, R.65, Y.77, D.119, D.124, K.126, Y.163, K.164 Ligands: NA.2 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:E.53, A:Y.77, A:Y.77, A:D.119, A:Y.163 Water bridges: A:R.65, A:R.65, A:R.65, A:R.65, A:Y.73, A:Y.73, A:D.89, A:D.89, A:D.124, A:D.124 Salt bridges: A:K.51, A:K.51, A:R.65, A:K.126, A:K.164 POP.11: 9 residues within 4Å: Chain B: K.51, R.65, Y.77, D.119, D.124, K.126, Y.163, K.164 Ligands: NA.9 20 PLIP interactions: 20 interactions with chain B Hydrogen bonds: B:E.53, B:Y.77, B:Y.77, B:D.119, B:Y.163 Water bridges: B:R.65, B:R.65, B:R.65, B:R.65, B:Y.73, B:Y.73, B:D.89, B:D.89, B:D.124, B:D.124 Salt bridges: B:K.51, B:K.51, B:R.65, B:K.126, B:K.164 POP.18: 9 residues within 4Å: Chain C: K.51, R.65, Y.77, D.119, D.124, K.126, Y.163, K.164 Ligands: NA.16 20 PLIP interactions: 20 interactions with chain C Hydrogen bonds: C:E.53, C:Y.77, C:Y.77, C:D.119, C:Y.163 Water bridges: C:R.65, C:R.65, C:R.65, C:R.65, C:Y.73, C:Y.73, C:D.89, C:D.89, C:D.124, C:D.124 Salt bridges: C:K.51, C:K.51, C:R.65, C:K.126, C:K.164 POP.25: 9 residues within 4Å: Chain D: K.51, R.65, Y.77, D.119, D.124, K.126, Y.163, K.164 Ligands: NA.23 12 PLIP interactions: 12 interactions with chain D Hydrogen bonds: D:Y.77, D:Y.163 Water bridges: D:R.65, D:R.65, D:D.89, D:D.92, D:K.170 Salt bridges: D:K.51, D:K.51, D:R.65, D:K.126, D:K.164 POP.32: 9 residues within 4Å: Chain E: K.51, R.65, Y.77, D.119, D.124, K.126, Y.163, K.164 Ligands: NA.30 12 PLIP interactions: 12 interactions with chain E Hydrogen bonds: E:Y.77, E:Y.163 Water bridges: E:R.65, E:R.65, E:D.89, E:D.92, E:K.170 Salt bridges: E:K.51, E:K.51, E:R.65, E:K.126, E:K.164 POP.39: 9 residues within 4Å: Chain F: K.51, R.65, Y.77, D.119, D.124, K.126, Y.163, K.164 Ligands: NA.37 12 PLIP interactions: 12 interactions with chain F Hydrogen bonds: F:Y.77, F:Y.163 Water bridges: F:R.65, F:R.65, F:D.89, F:D.92, F:K.170 Salt bridges: F:K.51, F:K.51, F:R.65, F:K.126, F:K.164

6 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.5: 4 residues within 4Å: Chain A: P.34, Q.35, D.181, H.184 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.181 PG4.12: 4 residues within 4Å: Chain B: P.34, Q.35, D.181, H.184 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.181 PG4.19: 4 residues within 4Å: Chain C: P.34, Q.35, D.181, H.184 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.181 PG4.26: 4 residues within 4Å: Chain D: P.34, Q.35, D.181, H.184 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.181, D:D.181, D:H.184 PG4.33: 4 residues within 4Å: Chain E: P.34, Q.35, D.181, H.184 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:D.181, E:D.181, E:H.184 PG4.40: 4 residues within 4Å: Chain F: P.34, Q.35, D.181, H.184 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:D.181, F:D.181, F:H.184

12 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 4 residues within 4Å: Chain A: K.157, V.174, E.175, W.177 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.157 PEG.7: 5 residues within 4Å: Chain A: R.108, H.132, K.134, V.135 Chain B: V.63 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.108 PEG.13: 4 residues within 4Å: Chain B: K.157, V.174, E.175, W.177 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.157 PEG.14: 5 residues within 4Å: Chain B: R.108, H.132, K.134, V.135 Chain C: V.63 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.108 PEG.20: 4 residues within 4Å: Chain C: K.157, V.174, E.175, W.177 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.157 PEG.21: 5 residues within 4Å: Chain A: V.63 Chain C: R.108, H.132, K.134, V.135 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.108 PEG.27: 4 residues within 4Å: Chain D: K.157, V.174, E.175, W.177 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.157 PEG.28: 5 residues within 4Å: Chain D: R.108, H.132, K.134, V.135 Chain E: V.63 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain D Water bridges: E:D.64 Hydrogen bonds: D:R.108 PEG.34: 4 residues within 4Å: Chain E: K.157, V.174, E.175, W.177 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:K.157 PEG.35: 5 residues within 4Å: Chain E: R.108, H.132, K.134, V.135 Chain F: V.63 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain F Hydrogen bonds: E:R.108 Water bridges: F:D.64 PEG.41: 4 residues within 4Å: Chain F: K.157, V.174, E.175, W.177 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:K.157 PEG.42: 5 residues within 4Å: Chain D: V.63 Chain F: R.108, H.132, K.134, V.135 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain D Hydrogen bonds: F:R.108 Water bridges: D:D.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Van Voorhis, W.C. et al., The role of medical structural genomics in discovering new drugs for infectious diseases. PLoS Comput Biol (2009)

Release Date

2008-09-30

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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