SMTL ID : 8a1z.1

Crystal structure of Phosphoserine phosphatase SerB from Mycobacterium avium in complex with 1-(2,4-dichlorophenyl)-3-hydroxyurea

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.28 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.191, D.193, D.347 Ligands: KVU.2 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.191, A:D.191, A:D.193, A:D.347, H2O.2 MG.4: 4 residues within 4Å: Chain B: D.191, D.193, D.347 Ligands: KVU.5 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.191, B:D.191, B:D.193, B:D.347, H2O.7

2 x KVU: 1-(2,4-dichlorophenyl)-3-oxidanyl-urea(Non-covalent)

KVU.2: 15 residues within 4Å: Chain A: D.191, D.193, S.194, E.200, I.202, T.219, M.223, F.229, L.233, R.236, G.280, G.281, F.282, D.347 Ligands: MG.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:D.193, A:I.202, A:F.229, A:L.233 Hydrogen bonds: A:D.193, A:E.200, A:E.200 Water bridges: A:V.192, A:K.324, A:G.348 KVU.5: 15 residues within 4Å: Chain B: D.191, D.193, S.194, E.200, I.202, T.219, M.223, F.229, L.233, R.236, G.280, G.281, F.282, D.347 Ligands: MG.4 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:D.193, B:I.202, B:F.229, B:L.233 Hydrogen bonds: B:D.193, B:E.200, B:E.200 Water bridges: B:V.192, B:K.324, B:G.348

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

CL.3: 5 residues within 4Å: Chain A: F.282, R.283, R.284, E.302, L.303 Ligand excluded by PLIP CL.6: 5 residues within 4Å: Chain B: F.282, R.283, R.284, E.302, L.303 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Haufroid, M. et al., Targeting the phosphoserine phosphatase MtSerB2 for tuberculosis drug discovery, an hybrid knowledge based /fragment based approach. Eur.J.Med.Chem. (2022)

Release Date

2022-11-23

Peptides

Phosphoserine phosphatase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Phosphoserine phosphatase

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