SMTL ID : 6xef.1

Crystal structure of the PTP1B YopH WPD loop Chimera 4 bound to vanadate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

monomer

Ligands

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

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

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 6 residues within 4Å: Chain A: P.89, N.90, T.91, C.92, G.93 Ligands: BEN.5 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:P.89 MG.3: 3 residues within 4Å: Chain A: L.88, P.89, N.90 No protein-ligand interaction detected (PLIP)

1 x VO4: VANADATE ION(Non-covalent)

VO4.4: 10 residues within 4Å: Chain A: D.181, Q.182, C.215, S.216, A.217, G.218, I.219, G.220, R.221, Q.262 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:D.181, A:D.181, A:D.181, A:S.216, A:A.217, A:G.218, A:I.219, A:G.220, A:R.221, A:R.221, A:Q.262, A:Q.262 Water bridges: A:Q.182, A:Q.266

1 x BEN: BENZAMIDINE(Non-functional Binders)

BEN.5: 6 residues within 4Å: Chain A: P.89, C.92, Q.123, I.134, F.135 Ligands: MG.2 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.135 Hydrogen bonds: A:I.134, A:I.134

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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