SMTL ID : 3lny.1

Second PDZ domain from human PTP1E in complex with RA-GEF2 peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-hexamer

Ligands

6 x GLU- GLN- VAL- SER- ALA- VAL: Rap guanine nucleotide exchange factor 6(Non-covalent)

GLU-GLN-VAL-SER-ALA-VAL.1: 17 residues within 4Å: Chain A: S.17, L.18, G.19, I.20, S.21, V.22, T.23, G.24, N.27, T.28, S.29, V.30, K.38, H.71, V.75, L.78, R.79 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:I.20, A:T.23, A:L.78 Hydrogen bonds: A:S.17, A:L.18, A:G.19, A:I.20, A:I.20, A:V.22, A:V.22, A:G.24, A:N.27, A:H.71, A:R.79, A:R.79 Water bridges: A:T.28, A:H.71, A:K.72 GLU-GLN-VAL-SER-ALA-VAL.5: 17 residues within 4Å: Chain B: S.17, L.18, G.19, I.20, S.21, V.22, T.23, G.24, N.27, T.28, S.29, V.30, K.38, H.71, V.75, L.78, R.79 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:I.20, B:T.23, B:L.78 Hydrogen bonds: B:S.17, B:L.18, B:G.19, B:I.20, B:I.20, B:V.22, B:V.22, B:G.24, B:N.27, B:H.71, B:R.79, B:R.79 Water bridges: B:T.28, B:H.71, B:K.72 GLU-GLN-VAL-SER-ALA-VAL.9: 17 residues within 4Å: Chain C: S.17, L.18, G.19, I.20, S.21, V.22, T.23, G.24, N.27, T.28, S.29, V.30, K.38, H.71, V.75, L.78, R.79 18 PLIP interactions: 18 interactions with chain C Hydrophobic interactions: C:I.20, C:T.23, C:L.78 Hydrogen bonds: C:S.17, C:L.18, C:G.19, C:I.20, C:I.20, C:V.22, C:V.22, C:G.24, C:N.27, C:H.71, C:R.79, C:R.79 Water bridges: C:T.28, C:H.71, C:K.72 GLU-GLN-VAL-SER-ALA-VAL.13: 17 residues within 4Å: Chain D: S.17, L.18, G.19, I.20, S.21, V.22, T.23, G.24, N.27, T.28, S.29, V.30, K.38, H.71, V.75, L.78, R.79 18 PLIP interactions: 18 interactions with chain D Hydrophobic interactions: D:I.20, D:T.23, D:L.78 Hydrogen bonds: D:S.17, D:L.18, D:G.19, D:I.20, D:I.20, D:I.20, D:V.22, D:V.22, D:G.24, D:N.27, D:H.71, D:R.79, D:R.79 Water bridges: D:H.71, D:K.72 GLU-GLN-VAL-SER-ALA-VAL.17: 17 residues within 4Å: Chain E: S.17, L.18, G.19, I.20, S.21, V.22, T.23, G.24, N.27, T.28, S.29, V.30, K.38, H.71, V.75, L.78, R.79 18 PLIP interactions: 18 interactions with chain E Hydrophobic interactions: E:I.20, E:T.23, E:L.78 Hydrogen bonds: E:S.17, E:L.18, E:G.19, E:I.20, E:I.20, E:I.20, E:V.22, E:V.22, E:G.24, E:N.27, E:H.71, E:R.79, E:R.79 Water bridges: E:H.71, E:K.72 GLU-GLN-VAL-SER-ALA-VAL.21: 17 residues within 4Å: Chain F: S.17, L.18, G.19, I.20, S.21, V.22, T.23, G.24, N.27, T.28, S.29, V.30, K.38, H.71, V.75, L.78, R.79 18 PLIP interactions: 18 interactions with chain F Hydrophobic interactions: F:I.20, F:T.23, F:L.78 Hydrogen bonds: F:S.17, F:L.18, F:G.19, F:I.20, F:I.20, F:I.20, F:V.22, F:V.22, F:G.24, F:N.27, F:H.71, F:R.79, F:R.79 Water bridges: F:H.71, F:K.72

6 x SCN: THIOCYANATE ION(Non-functional Binders)

SCN.2: 8 residues within 4Å: Chain A: A.60, V.61, N.62, G.63, H.86, L.87, L.88 Chain E: I.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.86 SCN.6: 8 residues within 4Å: Chain B: A.60, V.61, N.62, G.63, H.86, L.87, L.88 Chain D: I.6 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:H.86 SCN.10: 8 residues within 4Å: Chain C: A.60, V.61, N.62, G.63, H.86, L.87, L.88 Chain F: I.6 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:H.86 SCN.14: 8 residues within 4Å: Chain B: I.6 Chain D: A.60, V.61, N.62, G.63, H.86, L.87, L.88 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:H.86 SCN.18: 8 residues within 4Å: Chain A: I.6 Chain E: A.60, V.61, N.62, G.63, H.86, L.87, L.88 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:H.86 SCN.22: 8 residues within 4Å: Chain C: I.6 Chain F: A.60, V.61, N.62, G.63, H.86, L.87, L.88 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:H.86

12 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 3 residues within 4Å: Chain A: E.76, T.77, N.80 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.77, A:T.77 Water bridges: A:T.77, A:T.77 SO4.4: 11 residues within 4Å: Chain A: A.12, Q.83, V.84 Chain B: A.12, Q.83, V.84 Chain C: A.12, Q.83, V.84 Ligands: SO4.8, SO4.12 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: B:Q.83, A:Q.83, C:Q.83 SO4.7: 3 residues within 4Å: Chain B: E.76, T.77, N.80 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.77, B:T.77 Water bridges: B:T.77, B:T.77 SO4.8: 11 residues within 4Å: Chain A: A.12, Q.83, V.84 Chain B: A.12, Q.83, V.84 Chain C: A.12, Q.83, V.84 Ligands: SO4.4, SO4.12 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: B:Q.83, A:Q.83, C:Q.83 SO4.11: 3 residues within 4Å: Chain C: E.76, T.77, N.80 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:T.77, C:T.77 Water bridges: C:T.77, C:T.77 SO4.12: 11 residues within 4Å: Chain A: A.12, Q.83, V.84 Chain B: A.12, Q.83, V.84 Chain C: A.12, Q.83, V.84 Ligands: SO4.4, SO4.8 3 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: B:Q.83, A:Q.83, C:Q.83 SO4.15: 3 residues within 4Å: Chain D: E.76, T.77, N.80 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:T.77, D:T.77 Water bridges: D:T.77, D:T.77 SO4.16: 11 residues within 4Å: Chain D: A.12, Q.83, V.84 Chain E: A.12, Q.83, V.84 Chain F: A.12, Q.83, V.84 Ligands: SO4.20, SO4.24 3 PLIP interactions: 1 interactions with chain D, 1 interactions with chain E, 1 interactions with chain F Hydrogen bonds: D:Q.83, E:Q.83, F:Q.83 SO4.19: 3 residues within 4Å: Chain E: E.76, T.77, N.80 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:T.77, E:T.77 Water bridges: E:T.77, E:T.77 SO4.20: 11 residues within 4Å: Chain D: A.12, Q.83, V.84 Chain E: A.12, Q.83, V.84 Chain F: A.12, Q.83, V.84 Ligands: SO4.16, SO4.24 3 PLIP interactions: 1 interactions with chain D, 1 interactions with chain E, 1 interactions with chain F Hydrogen bonds: D:Q.83, E:Q.83, F:Q.83 SO4.23: 3 residues within 4Å: Chain F: E.76, T.77, N.80 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:T.77, F:T.77 Water bridges: F:T.77, F:T.77 SO4.24: 11 residues within 4Å: Chain D: A.12, Q.83, V.84 Chain E: A.12, Q.83, V.84 Chain F: A.12, Q.83, V.84 Ligands: SO4.16, SO4.20 3 PLIP interactions: 1 interactions with chain E, 1 interactions with chain F, 1 interactions with chain D Hydrogen bonds: E:Q.83, F:Q.83, D:Q.83

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, J. et al., Crystallographic and nuclear magnetic resonance evaluation of the impact of peptide binding to the second PDZ domain of protein tyrosine phosphatase 1E. Biochemistry (2010)

Release Date

2010-03-23

Peptides

Tyrosine-protein phosphatase non-receptor type 13: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

E
A

F
A

Tyrosine-protein phosphatase non-receptor type 13

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