SMTL ID : 6xed.1

Crystal Structure of the PTP1B YopH WPD loop Chimera 3 bound to tungstate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x WO4: TUNGSTATE(VI)ION(Non-covalent)

WO4.1: 7 residues within 4Å: Chain A: C.215, S.216, A.217, G.218, I.219, G.220, R.221 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.216, A:A.217, A:G.218, A:I.219, A:G.220, A:R.221, A:R.221 Water bridges: A:Q.182, A:Q.182, A:Q.262, A:Q.266

2 x BEN: BENZAMIDINE(Non-functional Binders)

BEN.2: 9 residues within 4Å: Chain A: R.112, I.149, K.150, S.151, Y.152, Y.153, T.154, H.175, G.177 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.150 Water bridges: A:S.151, A:T.154 pi-Stacking: A:H.175 BEN.4: 6 residues within 4Å: Chain A: P.89, C.92, Q.123, M.133, I.134, F.135 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.135 Hydrogen bonds: A:I.134, A:I.134

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.3: 1 residues within 4Å: Chain A: H.54 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.54, A:H.54

4 x MG: MAGNESIUM ION(Non-covalent)

MG.5: 3 residues within 4Å: Chain A: T.183, A.184, D.265 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.265 MG.6: 4 residues within 4Å: Chain A: E.115, K.116, P.180, D.181 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.181, H2O.11 MG.7: 3 residues within 4Å: Chain A: E.2, M.3, E.6 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.2, A:E.6, H2O.6 MG.8: 3 residues within 4Å: Chain A: W.100, T.165, E.167 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.165, A:E.167, H2O.6

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shen, R. et al., Insights into the importance of WPD-loop sequence for activity and structure in protein tyrosine phosphatases. Chem Sci (2022)

Release Date

2021-12-15

Peptides

Tyrosine-protein phosphatase non-receptor type 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Tyrosine-protein phosphatase non-receptor type 1

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