SMTL ID : 5zkk.1

Crystal structure of Phosphoserine phosphatase from Entamoeba histolytica

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x BME: BETA-MERCAPTOETHANOL(Non-functional Binders)

BME.1: 2 residues within 4Å: Chain A: C.23, E.79 No protein-ligand interaction detected (PLIP) BME.9: 3 residues within 4Å: Chain B: C.23, K.78, E.79 2 PLIP interactions: 2 interactions with chain B Water bridges: B:K.78, B:K.78

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

PO4.2: 9 residues within 4Å: Chain A: R.8, H.9, N.15, Q.21, R.57, E.79, H.146, G.147 Ligands: 144.6 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:N.15, A:Q.21, A:Q.21, A:E.79, A:G.147 Water bridges: A:Q.21, A:Q.21 Salt bridges: A:R.8, A:H.9, A:R.57, A:H.146 PO4.13: 8 residues within 4Å: Chain B: R.8, H.9, N.15, Q.21, R.57, E.79, H.146, G.147 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:N.15, B:E.79, B:E.79, B:E.79, B:G.147 Water bridges: B:Q.21, B:G.22 Salt bridges: B:R.8, B:H.9, B:R.57, B:H.146

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

PEG.3: 5 residues within 4Å: Chain A: G.45, N.46, F.47, D.48, T.140 No protein-ligand interaction detected (PLIP) PEG.4: 7 residues within 4Å: Chain A: A.126, L.130, G.156, L.157, E.159, G.183, P.185 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.183 PEG.5: 4 residues within 4Å: Chain A: K.3, I.5, N.46, T.177 5 PLIP interactions: 4 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.3, A:N.46 Water bridges: A:T.188, A:S.189, B:T.193 PEG.10: 1 residues within 4Å: Chain B: K.123 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.123 PEG.11: 5 residues within 4Å: Chain B: K.3, I.5, I.43, T.177, T.188 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.3 Water bridges: B:K.3, B:T.188

1 x 144: TRIS-HYDROXYMETHYL-METHYL-AMMONIUM(Non-covalent)

144.6: 7 residues within 4Å: Chain A: R.8, F.82, F.90, G.147, A.148, Y.165 Ligands: PO4.2 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.165, A:Y.165 Water bridges: A:R.8, A:Q.21, A:Q.21

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 6 residues within 4Å: Chain A: T.2, L.130, C.133, E.137, F.180, G.183 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.2, A:T.2, A:L.130 GOL.12: 7 residues within 4Å: Chain B: T.2, L.130, C.133, K.134, E.137, F.180, G.183 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.2, B:C.133

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.8: 5 residues within 4Å: Chain A: I.33, N.37, I.60, Q.63, K.64 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.64 PG4.14: 4 residues within 4Å: Chain B: I.33, I.60, Q.63, K.64 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kumari, P. et al., Structural and functional characterisation of phosphoserine phosphatase, that plays critical role in the oxidative stress response in the parasite Entamoeba histolytica. J.Struct.Biol. (2019)

Release Date

2019-04-03

Peptides

Phosphoglycerate mutase family protein, putative: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Phosphoglycerate mutase family protein, putative

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