SMTL ID : 8ael.1

SYNJ2BP complex with a synthetic Vangl2 peptide (3mer).

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

monomer

Ligands

1 x GLY- GLY- GLY- THR- SER- VAL: GLY-GLY-GLY-THR-SER-VAL(Non-covalent)

GLY-GLY-GLY-THR-SER-VAL.1: 11 residues within 4Å: Chain A: G.17, L.18, G.19, F.20, N.21, I.22, V.23, H.73, V.77, F.80, R.81 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.20, A:V.77, A:F.80, A:F.80 Hydrogen bonds: A:L.18, A:G.19, A:F.20, A:F.20, A:I.22, A:I.22, A:H.73, A:R.81, A:R.81 Water bridges: A:R.13

4 x CA: CALCIUM ION(Non-covalent)

CA.2: 3 residues within 4Å: Chain A: G.128, V.129, E.131 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:G.128, A:V.129, A:E.131 CA.3: 4 residues within 4Å: Chain A: K.166, L.169, S.170, E.174 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:K.166, A:L.169, A:E.174, H2O.2 CA.4: 5 residues within 4Å: Chain A: G.280, V.281, R.283, G.285, E.325 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:G.280, A:R.283, A:G.285, A:E.325, H2O.8 CA.5: 4 residues within 4Å: Chain A: M.356, G.358, G.360, D.400 5 PLIP interactions: 5 interactions with chain A Metal complexes: A:M.356, A:G.358, A:G.360, A:D.400, A:D.400

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 10 residues within 4Å: Chain A: C.211, S.212, R.213, T.214, L.252, R.257, V.300, L.337, C.340, K.344 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.257, A:K.344, A:K.344 Water bridges: A:R.213 GOL.7: 8 residues within 4Å: Chain A: P.184, A.185, D.188, R.213, E.217, S.372, R.373, V.376 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.372, A:R.373, A:R.373 Water bridges: A:R.213, A:R.213 GOL.8: 2 residues within 4Å: Chain A: N.10, R.53 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.8, A:N.10, A:R.53, A:R.53 GOL.9: 8 residues within 4Å: Chain A: A.258, E.259, G.261, D.265, L.268, R.298, S.299, H.302 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:G.261, A:D.265, A:D.265, A:S.299, A:S.299

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

2023-08-16

Peptides

Synaptojanin-2-binding protein,Annexin A2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Synaptojanin-2-binding protein,Annexin A2