SMTL ID : 3gvf.1 (1 other biounit)

1.7 Angstrom crystal structure of inorganic pyrophosphatase from burkholderia pseudomallei bound with phosphate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-hexamer

Ligands

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

PO4.1: 6 residues within 4Å: Chain A: K.51, E.53, R.65, E.120, Y.163, K.164 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:E.53, A:E.53, A:Y.77, A:Y.163, A:Y.163 Water bridges: A:K.51, A:D.119, A:D.119, A:D.119 Salt bridges: A:K.51, A:R.65, A:K.126, A:K.164 PO4.7: 6 residues within 4Å: Chain B: K.51, E.53, R.65, E.120, Y.163, K.164 13 PLIP interactions: 13 interactions with chain B Hydrogen bonds: B:E.53, B:E.53, B:Y.77, B:Y.163, B:Y.163 Water bridges: B:K.51, B:D.119, B:D.119, B:D.119 Salt bridges: B:K.51, B:R.65, B:K.126, B:K.164 PO4.13: 6 residues within 4Å: Chain C: K.51, E.53, R.65, E.120, Y.163, K.164 13 PLIP interactions: 13 interactions with chain C Hydrogen bonds: C:E.53, C:E.53, C:Y.77, C:Y.163, C:Y.163 Water bridges: C:K.51, C:D.119, C:D.119, C:D.119 Salt bridges: C:K.51, C:R.65, C:K.126, C:K.164 PO4.19: 6 residues within 4Å: Chain D: K.51, E.53, R.65, E.120, Y.163, K.164 10 PLIP interactions: 10 interactions with chain D Hydrogen bonds: D:E.53, D:Y.163 Water bridges: D:K.51, D:Y.163, D:Y.163, D:Y.163 Salt bridges: D:K.51, D:R.65, D:K.126, D:K.164 PO4.25: 6 residues within 4Å: Chain E: K.51, E.53, R.65, E.120, Y.163, K.164 10 PLIP interactions: 10 interactions with chain E Hydrogen bonds: E:E.53, E:Y.163 Water bridges: E:K.51, E:Y.163, E:Y.163, E:Y.163 Salt bridges: E:K.51, E:R.65, E:K.126, E:K.164 PO4.31: 6 residues within 4Å: Chain F: K.51, E.53, R.65, E.120, Y.163, K.164 10 PLIP interactions: 10 interactions with chain F Hydrogen bonds: F:E.53, F:Y.163 Water bridges: F:K.51, F:Y.163, F:Y.163, F:Y.163 Salt bridges: F:K.51, F:R.65, F:K.126, F:K.164

6 x K: POTASSIUM ION(Non-covalent)

K.2: 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.14: 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.20: 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.26: 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.32: 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

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

NA.3: 4 residues within 4Å: Chain A: D.87, D.92, D.124, K.126 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.126, A:K.126 Water bridges: A:S.85, A:D.87, A:D.92 NA.9: 4 residues within 4Å: Chain B: D.87, D.92, D.124, K.126 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.87, B:K.126 Water bridges: B:S.85, B:D.87, B:D.92 NA.15: 4 residues within 4Å: Chain C: D.87, D.92, D.124, K.126 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:D.87, C:K.126 Water bridges: C:S.85, C:D.87, C:D.92 NA.21: 4 residues within 4Å: Chain D: D.87, D.92, D.124, K.126 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:K.126, D:K.126 Water bridges: D:S.85, D:D.92 NA.27: 4 residues within 4Å: Chain E: D.87, D.92, D.124, K.126 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:D.92, E:K.126 Water bridges: E:S.85, E:D.92 NA.33: 4 residues within 4Å: Chain F: D.87, D.92, D.124, K.126 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:D.124, F:K.126 Water bridges: F:S.85, F:D.92

12 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.4: 3 residues within 4Å: Chain A: I.180, D.181 Ligands: PGE.6 No protein-ligand interaction detected (PLIP) PGE.6: 4 residues within 4Å: Chain A: Q.35, D.181, H.184 Ligands: PGE.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.181 PGE.10: 3 residues within 4Å: Chain B: I.180, D.181 Ligands: PGE.12 No protein-ligand interaction detected (PLIP) PGE.12: 4 residues within 4Å: Chain B: Q.35, D.181, H.184 Ligands: PGE.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:D.181 PGE.16: 3 residues within 4Å: Chain C: I.180, D.181 Ligands: PGE.18 No protein-ligand interaction detected (PLIP) PGE.18: 4 residues within 4Å: Chain C: Q.35, D.181, H.184 Ligands: PGE.16 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.181 PGE.22: 3 residues within 4Å: Chain D: I.180, D.181 Ligands: PGE.24 No protein-ligand interaction detected (PLIP) PGE.24: 4 residues within 4Å: Chain D: Q.35, D.181, H.184 Ligands: PGE.22 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.181, D:D.181, D:H.184 PGE.28: 3 residues within 4Å: Chain E: I.180, D.181 Ligands: PGE.30 No protein-ligand interaction detected (PLIP) PGE.30: 4 residues within 4Å: Chain E: Q.35, D.181, H.184 Ligands: PGE.28 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:D.181, E:D.181, E:H.184 PGE.34: 3 residues within 4Å: Chain F: I.180, D.181 Ligands: PGE.36 No protein-ligand interaction detected (PLIP) PGE.36: 4 residues within 4Å: Chain F: Q.35, D.181, H.184 Ligands: PGE.34 3 PLIP interactions: 3 interactions with chain F Hydrogen bonds: F:D.181, F:D.181, F:H.184

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

PEG.5: 4 residues within 4Å: Chain A: K.157, V.174, E.175, W.177 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.157, A:V.174 Water bridges: A:D.154, A:W.177 PEG.11: 4 residues within 4Å: Chain B: K.157, V.174, E.175, W.177 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.157, B:V.174 Water bridges: B:D.154, B:W.177 PEG.17: 4 residues within 4Å: Chain C: K.157, V.174, E.175, W.177 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.157, C:V.174 Water bridges: C:D.154, C:W.177 PEG.23: 4 residues within 4Å: Chain D: K.157, V.174, E.175, W.177 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:K.157, D:V.174 Water bridges: D:D.154, D:W.177 PEG.29: 4 residues within 4Å: Chain E: K.157, V.174, E.175, W.177 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:K.157, E:V.174 Water bridges: E:D.154, E:W.177 PEG.35: 4 residues within 4Å: Chain F: K.157, V.174, E.175, W.177 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:K.157, F:V.174 Water bridges: F:D.154, F:W.177

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Baugh, L. et al., Combining functional and structural genomics to sample the essential Burkholderia structome. Plos One (2013)

Release Date

2009-04-28

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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