SMTL ID : 3qu2.6 (5 other biounits)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-tetramer

Ligands

4 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 5 residues within 4Å: Chain A: D.30, D.32, E.66, E.190, N.191 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.30, A:D.32, A:E.66, H2O.5 MG.4: 5 residues within 4Å: Chain B: D.30, D.32, E.66, E.190, 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.8, H2O.9 MG.8: 5 residues within 4Å: Chain C: D.30, D.32, E.66, E.190, N.191 5 PLIP interactions: 3 interactions with chain C, 2 Ligand-Water interactions Metal complexes: C:D.30, C:D.32, C:E.66, H2O.18, H2O.18 MG.11: 5 residues within 4Å: Chain D: D.30, D.32, E.66, E.190, N.191 4 PLIP interactions: 3 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.30, D:D.32, D:E.66, H2O.21

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 7 residues within 4Å: Chain A: N.210, G.216, L.227, P.229 Chain D: D.225, L.226, L.227 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain D Hydrogen bonds: A:N.210, A:G.216, D:L.227, D:L.227 GOL.5: 8 residues within 4Å: Chain B: D.32, M.39, H.42, W.46, E.66, G.67, R.68 Ligands: CL.7 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.32, B:D.32, B:G.67, B:R.68 Water bridges: B:W.46 GOL.6: 7 residues within 4Å: Chain B: N.210, G.216, L.227, P.229 Chain C: D.225, L.226, L.227 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain B Hydrogen bonds: C:L.227, C:L.227, B:N.210, B:G.216 Water bridges: B:N.210 GOL.9: 7 residues within 4Å: Chain B: L.220, L.226, L.227 Chain C: N.210, G.216, L.227, P.229 7 PLIP interactions: 5 interactions with chain C, 2 interactions with chain B Hydrogen bonds: C:N.210, C:G.216, B:L.227, B:L.227 Water bridges: C:N.210, C:N.210, C:L.214 GOL.10: 8 residues within 4Å: Chain C: D.32, H.42, W.46, E.66, G.67, R.68, G.133, S.134 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:D.32, C:W.46, C:G.67 Water bridges: C:D.30, C:D.32, C:T.73, C:T.132, C:G.133 GOL.12: 7 residues within 4Å: Chain D: D.32, H.42, W.46, H.65, E.66, G.67, R.68 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:D.32, D:W.46, D:H.65, D:G.67 GOL.13: 7 residues within 4Å: Chain A: L.220, L.226, L.227 Chain D: N.210, G.216, L.227, P.229 4 PLIP interactions: 2 interactions with chain D, 2 interactions with chain A Hydrogen bonds: D:N.210, D:G.216, A:L.227, A:L.227 GOL.14: 7 residues within 4Å: Chain D: L.140, L.143, E.144, F.151, H.152, K.153, M.156 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:L.140, D:E.144 Water bridges: D:H.152

1 x CIT: CITRIC ACID(Non-functional Binders)

CIT.3: 10 residues within 4Å: Chain A: D.32, M.39, H.42, W.46, E.66, G.67, R.68, K.98, G.133, S.134 16 PLIP interactions: 16 interactions with chain A Hydrogen bonds: A:D.32, A:G.67, A:R.68, A:G.133 Water bridges: A:H.42, A:Y.95, A:K.98, A:K.98, A:T.132, A:T.132, A:T.132, A:S.134 Salt bridges: A:H.42, A:H.42, A:K.98, A:K.98

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

CL.7: 5 residues within 4Å: Chain B: D.30, T.132, G.133, K.166 Ligands: GOL.5 Ligand excluded by PLIP

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
C

D
D

INORGANIC PYROPHOSPHATASE

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