SMTL ID : 7r2t.1

SYNJ2BP complex with a phosphorylated Vangl2 peptide at the P-1 position.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

1 x SER- GLU- THR- SEP- VAL: Vangle2 peptide binding motif with the P-1 phosphrylated(Non-covalent)

SER-GLU-THR-SEP-VAL.1: 13 residues within 4Å: Chain A: G.22, L.23, G.24, F.25, N.26, I.27, V.28, Q.33, R.46, H.78, V.82, F.85, R.86 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:I.27, A:V.28, A:V.82, A:F.85, A:F.85 Hydrogen bonds: A:L.23, A:G.24, A:F.25, A:F.25, A:N.26, A:I.27, A:I.27, A:H.78, A:R.86 Salt bridges: A:R.46

5 x CA: CALCIUM ION(Non-covalent)(Non-functional Binders)

CA.2: 2 residues within 4Å: Chain A: G.133, E.136 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:G.133, A:E.136 CA.3: 5 residues within 4Å: Chain A: G.285, R.288, K.289, G.290, E.330 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:G.285, A:R.288, A:E.330, H2O.1, H2O.1 CA.4: 4 residues within 4Å: Chain A: M.361, G.363, G.365, D.405 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:M.361, A:G.363, A:G.365, A:D.405 CA.7: 2 residues within 4Å: Chain A: R.279, K.287 No protein-ligand interaction detected (PLIP) CA.8: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 7 residues within 4Å: Chain A: P.189, D.193, R.218, E.222, S.377, R.378, V.381 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.377, A:R.378 GOL.6: 8 residues within 4Å: Chain A: C.216, S.217, R.218, R.262, V.305, L.342, C.345, K.349 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.262, A:K.349 Water bridges: A:N.220

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Carrasco, K. et al., SYNJ2BP PDZ domain in complex with a synthetic Vangl2 peptide. To Be Published

Release Date

2023-05-17

Peptides

Synaptojanin-2-binding protein,Annexin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Synaptojanin-2-binding protein,Annexin

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