SMTL ID : 3qxg.1 (3 other biounits)

Crystal structure of pyrophosphatase from bacteroides thetaiotaomicron complexed with calcium, a closed cap conformation

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.24 Å

Oligo State

homo-tetramer

Ligands

10 x ACT: ACETATE ION(Non-functional Binders)

ACT.1: 5 residues within 4Å: Chain A: N.210, D.215, G.216 Chain D: L.220, D.225 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:N.210, A:G.216 Hydrophobic interactions: D:L.220 ACT.6: 7 residues within 4Å: Chain A: D.30, G.67, T.132, G.133, S.134, K.166 Ligands: PO4.4 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.133 Water bridges: A:D.30, A:D.30, A:D.32, A:K.166, A:E.190 Salt bridges: A:K.166 ACT.7: 4 residues within 4Å: Chain A: H.42, W.46, R.68, K.98 4 PLIP interactions: 4 interactions with chain A Water bridges: A:Y.95, A:S.134 Salt bridges: A:H.42, A:K.98 ACT.9: 6 residues within 4Å: Chain B: D.30, G.67, T.132, G.133, S.134, K.166 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.133 Water bridges: B:M.31, B:M.31, B:G.67 Salt bridges: B:K.166 ACT.12: 5 residues within 4Å: Chain B: N.210, D.215, G.216 Chain C: L.220, D.225 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain C Hydrogen bonds: B:N.210, B:G.216 Water bridges: B:L.214, B:D.215, C:D.225 Hydrophobic interactions: C:L.220 ACT.16: 5 residues within 4Å: Chain B: L.220, D.225 Chain C: N.210, D.215, G.216 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B Hydrogen bonds: C:N.210, C:G.216 Hydrophobic interactions: B:L.220 ACT.21: 7 residues within 4Å: Chain C: D.30, G.67, T.132, G.133, S.134, K.166 Ligands: PO4.19 9 PLIP interactions: 9 interactions with chain C Hydrogen bonds: C:T.132, C:G.133 Water bridges: C:D.30, C:D.30, C:D.32, C:D.32, C:K.166, C:E.190 Salt bridges: C:K.166 ACT.22: 4 residues within 4Å: Chain C: H.42, W.46, R.68, K.98 4 PLIP interactions: 4 interactions with chain C Water bridges: C:Y.95, C:Y.95 Salt bridges: C:H.42, C:K.98 ACT.24: 6 residues within 4Å: Chain D: D.30, G.67, T.132, G.133, S.134, K.166 7 PLIP interactions: 7 interactions with chain D Hydrogen bonds: D:T.132, D:G.133 Water bridges: D:M.31, D:M.31, D:D.32, D:G.67 Salt bridges: D:K.166 ACT.27: 5 residues within 4Å: Chain A: L.220, D.225 Chain D: N.210, D.215, G.216 6 PLIP interactions: 4 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:N.210, D:G.216 Water bridges: D:L.214, D:D.215, A:D.225 Hydrophobic interactions: A:L.220

14 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.2: 1 residues within 4Å: Chain A: P.213 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:P.213, H2O.6, H2O.6, H2O.6, H2O.6 CA.3: 5 residues within 4Å: Chain A: D.30, D.32, E.66, N.191 Ligands: PO4.4 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.30, A:D.32, A:E.66, H2O.1, H2O.6 CA.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.13: 1 residues within 4Å: Chain B: P.213 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:P.213, H2O.12, H2O.13, H2O.13, H2O.19 CA.14: 4 residues within 4Å: Chain B: D.30, D.32, E.66, N.191 5 PLIP interactions: 3 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.30, B:D.32, B:E.66, H2O.11, H2O.11 CA.15: 4 residues within 4Å: Chain B: E.197, K.201 Ligands: TLA.5, MG.8 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.197, H2O.7, H2O.17, H2O.17, H2O.17 CA.17: 1 residues within 4Å: Chain C: P.213 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:P.213, H2O.26, H2O.27, H2O.27, H2O.27 CA.18: 5 residues within 4Å: Chain C: D.30, D.32, E.66, N.191 Ligands: PO4.19 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.30, C:D.32, C:E.66, H2O.21, H2O.26 CA.25: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.26: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) CA.28: 1 residues within 4Å: Chain D: P.213 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:P.213, H2O.32, H2O.33, H2O.33, H2O.39 CA.29: 4 residues within 4Å: Chain D: D.30, D.32, E.66, N.191 5 PLIP interactions: 3 interactions with chain D, 2 Ligand-Water interactions Metal complexes: D:D.30, D:D.32, D:E.66, H2O.31, H2O.31 CA.30: 4 residues within 4Å: Chain D: E.197, K.201 Ligands: TLA.20, MG.23 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:E.197, H2O.27, H2O.37, H2O.37, H2O.37

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

PO4.4: 9 residues within 4Å: Chain A: D.30, M.31, D.32, E.66, G.67, T.132, K.166 Ligands: CA.3, ACT.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:M.31, A:D.32, A:T.132 Salt bridges: A:K.166 PO4.19: 9 residues within 4Å: Chain C: D.30, M.31, D.32, E.66, G.67, T.132, K.166 Ligands: CA.18, ACT.21 7 PLIP interactions: 7 interactions with chain C Hydrogen bonds: C:M.31, C:D.32, C:D.32, C:E.66, C:T.132, C:T.132 Salt bridges: C:K.166

2 x TLA: L(+)-TARTARIC ACID(Non-covalent)

TLA.5: 10 residues within 4Å: Chain A: R.68, P.167, E.197, K.201 Chain B: R.68, P.167, E.197, K.201 Ligands: MG.8, CA.15 9 PLIP interactions: 5 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:E.197, B:E.197 Water bridges: A:K.201, A:K.201, B:K.201 Salt bridges: A:R.68, A:K.201, B:R.68, B:K.201 TLA.20: 10 residues within 4Å: Chain C: R.68, P.167, E.197, K.201 Chain D: R.68, P.167, E.197, K.201 Ligands: MG.23, CA.30 13 PLIP interactions: 7 interactions with chain C, 6 interactions with chain D Hydrogen bonds: C:E.197, D:E.197 Water bridges: C:E.197, C:E.197, C:K.201, C:K.201, D:E.197, D:E.197, D:K.201 Salt bridges: C:R.68, C:K.201, D:R.68, D:K.201

2 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 4 residues within 4Å: Chain A: E.197, K.201 Ligands: TLA.5, CA.15 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.197, H2O.1, H2O.7, H2O.17 MG.23: 4 residues within 4Å: Chain C: E.197, K.201 Ligands: TLA.20, CA.30 4 PLIP interactions: 1 interactions with chain C, 3 Ligand-Water interactions Metal complexes: C:E.197, H2O.22, H2O.27, H2O.37

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, H. et al., Divergence of Structure and Function in the Haloacid Dehalogenase Enzyme Superfamily: Bacteroides thetaiotaomicron BT2127 Is an Inorganic Pyrophosphatase. Biochemistry (2011)

Release Date

2011-04-27

Peptides

INORGANIC PYROPHOSPHATASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

INORGANIC PYROPHOSPHATASE

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