SMTL ID : 6k27.4 (3 other biounits)

Pyrophosphatase with PPi from Acinetobacter baumannii

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

homo-hexamer

Ligands

6 x DPO: DIPHOSPHATE(Non-covalent)

DPO.1: 11 residues within 4Å: Chain A: K.33, E.35, R.47, Y.59, D.106, K.108, Y.145, K.146 Ligands: MG.2, MG.3, MG.4 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:E.35, A:Y.59, A:Y.145 Salt bridges: A:K.33, A:K.33, A:R.47, A:K.108, A:K.146 DPO.5: 11 residues within 4Å: Chain B: K.33, E.35, R.47, Y.59, D.106, K.108, Y.145, K.146 Ligands: MG.6, MG.7, MG.8 6 PLIP interactions: 6 interactions with chain B Salt bridges: B:K.33, B:K.33, B:R.47, B:K.108, B:K.146, B:K.152 DPO.9: 11 residues within 4Å: Chain C: K.33, E.35, R.47, Y.59, D.106, K.108, Y.145, K.146 Ligands: MG.10, MG.11, MG.12 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:E.35, C:Y.59, C:Y.145 Salt bridges: C:K.33, C:K.33, C:R.47, C:K.108, C:K.146 DPO.13: 11 residues within 4Å: Chain D: K.33, E.35, R.47, Y.59, D.106, K.108, Y.145, K.146 Ligands: MG.14, MG.15, MG.16 6 PLIP interactions: 6 interactions with chain D Salt bridges: D:K.33, D:K.33, D:R.47, D:K.108, D:K.146, D:K.152 DPO.17: 11 residues within 4Å: Chain E: K.33, E.35, R.47, Y.59, D.106, K.108, Y.145, K.146 Ligands: MG.18, MG.19, MG.20 8 PLIP interactions: 8 interactions with chain E Hydrogen bonds: E:E.35, E:Y.59, E:Y.145 Salt bridges: E:K.33, E:K.33, E:R.47, E:K.108, E:K.146 DPO.21: 11 residues within 4Å: Chain F: K.33, E.35, R.47, Y.59, D.106, K.108, Y.145, K.146 Ligands: MG.22, MG.23, MG.24 6 PLIP interactions: 6 interactions with chain F Salt bridges: F:K.33, F:K.33, F:R.47, F:K.108, F:K.146, F:K.152

18 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: Y.59, D.74 Ligands: DPO.1, MG.3 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:Y.59, A:D.74 MG.3: 6 residues within 4Å: Chain A: D.69, D.74, D.106, K.108 Ligands: DPO.1, MG.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.69, A:D.74, A:D.74 MG.4: 5 residues within 4Å: Chain A: D.101, D.106, K.108, K.146 Ligands: DPO.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:D.101, A:D.106 MG.6: 5 residues within 4Å: Chain B: D.101, D.106, K.108, K.146 Ligands: DPO.5 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.101, B:D.106 MG.7: 4 residues within 4Å: Chain B: Y.59, D.74 Ligands: DPO.5, MG.8 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:Y.59, B:D.74 MG.8: 6 residues within 4Å: Chain B: D.69, D.74, D.106, K.108 Ligands: DPO.5, MG.7 2 PLIP interactions: 2 interactions with chain B Metal complexes: B:D.74, B:D.74 MG.10: 4 residues within 4Å: Chain C: Y.59, D.74 Ligands: DPO.9, MG.11 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:Y.59, C:D.74 MG.11: 6 residues within 4Å: Chain C: D.69, D.74, D.106, K.108 Ligands: DPO.9, MG.10 3 PLIP interactions: 3 interactions with chain C Metal complexes: C:D.69, C:D.74, C:D.74 MG.12: 5 residues within 4Å: Chain C: D.101, D.106, K.108, K.146 Ligands: DPO.9 2 PLIP interactions: 2 interactions with chain C Metal complexes: C:D.101, C:D.106 MG.14: 5 residues within 4Å: Chain D: D.101, D.106, K.108, K.146 Ligands: DPO.13 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.101, D:D.106 MG.15: 4 residues within 4Å: Chain D: Y.59, D.74 Ligands: DPO.13, MG.16 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:Y.59, D:D.74 MG.16: 6 residues within 4Å: Chain D: D.69, D.74, D.106, K.108 Ligands: DPO.13, MG.15 2 PLIP interactions: 2 interactions with chain D Metal complexes: D:D.74, D:D.74 MG.18: 4 residues within 4Å: Chain E: Y.59, D.74 Ligands: DPO.17, MG.19 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:Y.59, E:D.74 MG.19: 6 residues within 4Å: Chain E: D.69, D.74, D.106, K.108 Ligands: DPO.17, MG.18 3 PLIP interactions: 3 interactions with chain E Metal complexes: E:D.69, E:D.74, E:D.74 MG.20: 5 residues within 4Å: Chain E: D.101, D.106, K.108, K.146 Ligands: DPO.17 2 PLIP interactions: 2 interactions with chain E Metal complexes: E:D.101, E:D.106 MG.22: 5 residues within 4Å: Chain F: D.101, D.106, K.108, K.146 Ligands: DPO.21 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.101, F:D.106 MG.23: 4 residues within 4Å: Chain F: Y.59, D.74 Ligands: DPO.21, MG.24 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:Y.59, F:D.74 MG.24: 6 residues within 4Å: Chain F: D.69, D.74, D.106, K.108 Ligands: DPO.21, MG.23 2 PLIP interactions: 2 interactions with chain F Metal complexes: F:D.74, F:D.74

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Si, Y. et al., Crystal Structures of Pyrophosphatase from Acinetobacter baumannii: Snapshots of Pyrophosphate Binding and Identification of a Phosphorylated Enzyme Intermediate. Int J Mol Sci (2019)

Release Date

2019-10-02

Peptides

Inorganic pyrophosphatase: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
H

C
D

D
H

E
D

F
H

Inorganic pyrophosphatase

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