SMTL ID : 5cux.1

Crystal structure of N-terminal domain truncated Trypanosoma cruzi Vacuolar Soluble Pyrophosphatases in complex with PPi

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.80 Å

Oligo State

homo-tetramer

Ligands

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

POP.1: 9 residues within 4Å: Chain A: V.63, R.68, K.70, L.74, P.75, M.76, N.77, R.78, H.191 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.77 Water bridges: A:R.197, A:R.197 Salt bridges: A:R.68, A:R.68, A:K.70, A:K.70, A:H.191 POP.2: 6 residues within 4Å: Chain A: K.92, R.114, D.178, Y.223, K.224 Ligands: PO4.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.114 Salt bridges: A:K.92, A:K.92, A:K.224 POP.7: 9 residues within 4Å: Chain B: V.63, R.68, K.70, L.74, P.75, M.76, N.77, R.78, H.191 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.77, B:R.78 Water bridges: B:R.197, B:R.197 Salt bridges: B:R.68, B:R.68, B:K.70, B:H.191 POP.11: 9 residues within 4Å: Chain C: V.63, R.68, K.70, L.74, P.75, M.76, N.77, R.78, H.191 8 PLIP interactions: 8 interactions with chain C Hydrogen bonds: C:N.77 Water bridges: C:R.197, C:R.197 Salt bridges: C:R.68, C:R.68, C:K.70, C:K.70, C:H.191 POP.12: 6 residues within 4Å: Chain C: K.92, R.114, D.178, Y.223, K.224 Ligands: PO4.15 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:R.114, C:Y.223 Salt bridges: C:K.92, C:K.92, C:K.224 POP.17: 9 residues within 4Å: Chain D: V.63, R.68, K.70, L.74, P.75, M.76, N.77, R.78, H.191 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:N.77, D:R.78 Water bridges: D:R.197, D:R.197 Salt bridges: D:R.68, D:R.68, D:K.70, D:H.191

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

PO4.3: 6 residues within 4Å: Chain A: T.69, K.70 Chain B: V.165, G.166, A.167, N.192 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:A.167, B:N.192, A:T.69 Salt bridges: A:K.70 PO4.4: 7 residues within 4Å: Chain A: P.206, L.209, P.210, G.211, C.212, L.213, D.214 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.211, A:L.213, A:D.214, A:D.214, A:D.214 PO4.5: 4 residues within 4Å: Chain A: R.114, D.179, K.224 Ligands: POP.2 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.114, A:K.224 PO4.6: 3 residues within 4Å: Chain A: Y.62, R.64, H.254 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.64, A:H.254 PO4.8: 6 residues within 4Å: Chain A: V.165, G.166, A.167, N.192 Chain B: T.69, K.70 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:T.69, B:T.69, A:A.167, A:N.192 Salt bridges: B:K.70 Water bridges: A:S.190, A:S.190, A:N.192 PO4.9: 5 residues within 4Å: Chain B: R.114, D.178, Y.223, K.224 Ligands: PO4.10 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.223, B:Y.223, B:Y.223 Salt bridges: B:R.114, B:K.224 PO4.10: 3 residues within 4Å: Chain B: D.179, K.224 Ligands: PO4.9 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.179 Water bridges: B:K.224 Salt bridges: B:K.224 PO4.13: 6 residues within 4Å: Chain C: T.69, K.70 Chain D: V.165, G.166, A.167, N.192 5 PLIP interactions: 3 interactions with chain C, 2 interactions with chain D Hydrogen bonds: C:T.69, C:T.69, D:A.167, D:N.192 Salt bridges: C:K.70 PO4.14: 7 residues within 4Å: Chain C: P.206, L.209, P.210, G.211, C.212, L.213, D.214 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:G.211, C:L.213, C:D.214, C:D.214, C:D.214 PO4.15: 4 residues within 4Å: Chain C: R.114, D.179, K.224 Ligands: POP.12 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:R.114, C:K.224 PO4.16: 3 residues within 4Å: Chain C: Y.62, R.64, H.254 2 PLIP interactions: 2 interactions with chain C Salt bridges: C:R.64, C:H.254 PO4.18: 6 residues within 4Å: Chain C: V.165, G.166, A.167, N.192 Chain D: T.69, K.70 7 PLIP interactions: 2 interactions with chain D, 5 interactions with chain C Hydrogen bonds: D:T.69, C:A.167, C:N.192 Salt bridges: D:K.70 Water bridges: C:S.190, C:S.190, C:N.192 PO4.19: 5 residues within 4Å: Chain D: R.114, D.178, Y.223, K.224 Ligands: PO4.20 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:Y.223, D:Y.223 Salt bridges: D:R.114, D:K.224 PO4.20: 3 residues within 4Å: Chain D: D.179, K.224 Ligands: PO4.19 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:D.179 Water bridges: D:K.224 Salt bridges: D:K.224

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, Y.Y. et al., Crystal structure of Trypanosoma cruzi protein in complex with ligand. Acs Chem.Biol. (2016)

Release Date

2016-03-02

Peptides

Acidocalcisomal pyrophosphatase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Acidocalcisomal pyrophosphatase