SMTL ID : 7ft2.4 (3 other biounits)

SDCBP PanDDA analysis group deposition -- The PDZ domans of SDCBP in complex with Z235449082

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.04 Å

Oligo State

monomer

Ligands

1 x JFS: [4-(1H-benzimidazol-1-yl)phenyl]methanol(Non-covalent)

JFS.1: 4 residues within 4Å: Chain A: M.179, A.180, I.183, L.187 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.183, A:L.187 Hydrogen bonds: A:A.180 pi-Cation interactions: A:R.25, A:R.25

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 7 residues within 4Å: Chain A: R.50, G.140, Q.141, N.142, D.189, H.190, T.191 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.142, A:D.189 Water bridges: A:R.50, A:R.50 EDO.3: 3 residues within 4Å: Chain A: D.30, I.171, H.174 2 PLIP interactions: 2 interactions with chain A Water bridges: A:D.30, A:D.30

1 x ALA: ALANINE(Non-covalent)

ALA.4: 5 residues within 4Å: Chain A: H.105, V.106, G.107, F.108, L.155 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:L.155 Hydrogen bonds: A:V.106, A:G.107, A:F.108 Water bridges: A:H.105, A.4

1 x DGL: D-GLUTAMIC ACID(Non-covalent)

DGL.5: 7 residues within 4Å: Chain A: K.27, S.28, S.67, S.68, H.174, R.178 Ligands: GLY.6 11 PLIP interactions: 7 interactions with chain A, 4 Ligand-Ligand interactions Hydrogen bonds: A:S.28, A:S.68, G.6, G.6, G.6, G.6 Water bridges: A:D.69 Salt bridges: A:K.27, A:K.27, A:H.174, A:R.178

1 x GLY: GLYCINE(Non-covalent)

GLY.6: 5 residues within 4Å: Chain A: S.28, N.31, G.65, S.67 Ligands: DGL.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.28, A:S.28, A:G.65 Water bridges: A:S.67

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bradshaw, W.J. et al., SDCBP PanDDA analysis group deposition. To Be Published

Release Date

2023-02-15

Peptides

Syntenin-1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

Syntenin-1

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