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

SDCBP PanDDA analysis group deposition -- The PDZ domans of SDCBP in complex with Z1650168321

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

monomer

Ligands

1 x VW7: N-(8-methyl-1,2,3,4-tetrahydroquinolin-5-yl)acetamide(Non-covalent)

VW7.1: 5 residues within 4Å: Chain A: Q.141, D.153, I.154, T.157, H.190 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:I.154, A:T.157, A:H.190 Hydrogen bonds: A:Q.141 Water bridges: A:D.153

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

EDO.2: 6 residues within 4Å: Chain A: 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:E.137 EDO.3: 5 residues within 4Å: Chain A: I.29, D.30, F.170, I.171, H.174 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.30 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 8 PLIP interactions: 7 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:F.108, A:L.155 Hydrogen bonds: A:V.106, A:G.107, A:F.108 Water bridges: A:F.108, A.4 Salt bridges: A:H.105

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: 3 Ligand-Ligand interactions, 8 interactions with chain A Hydrogen bonds: G.6, G.6, A:S.68 Water bridges: G.6, A:K.27, A:S.28, A:D.69 Salt bridges: A:K.27, A:K.27, A:H.174, A:R.178

2 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:N.31, A:G.65 GLY.7: 8 residues within 4Å: Chain A: G.113, N.134, I.135, V.143, I.144, G.145, I.151, F.172 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.134, A:I.135, A:I.135, A:G.145

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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