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

SDCBP PanDDA analysis group deposition -- The PDZ domans of SDCBP in complex with Z729726784

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

monomer

Ligands

1 x YDU: 2-cyclopentyl-N-(3-methyl-1,2,4-oxadiazol-5-yl)acetamide(Non-covalent)

YDU.1: 5 residues within 4Å: Chain A: Q.141, H.190, T.191, I.192, V.195 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:H.190, A:I.192, A:V.195 Hydrogen bonds: A:I.192

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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.30

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

SO4.4: 4 residues within 4Å: Chain A: H.99, S.123, R.126, N.127 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:H.99, A:S.123, A:N.127 Water bridges: A:R.126 Salt bridges: A:H.99, A:R.126 SO4.5: 3 residues within 4Å: Chain A: N.112, K.147, D.148 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.112, A:N.112, A:D.148, A:D.148 Water bridges: A:S.149 SO4.6: 3 residues within 4Å: Chain A: S.45, L.46, G.48 3 PLIP interactions: 3 interactions with chain A Water bridges: A:G.48, A:T.191, A:T.191

1 x ALA: ALANINE(Non-covalent)

ALA.7: 6 residues within 4Å: Chain A: H.105, V.106, G.107, F.108, F.110, L.155 9 PLIP interactions: 7 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:F.108, A:F.110, A:L.155 Hydrogen bonds: A:V.106, A:G.107, A:F.108 Salt bridges: A:H.105 Water bridges: A.7, A.7

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

DGL.8: 7 residues within 4Å: Chain A: K.27, S.28, S.67, S.68, H.174, R.178 Ligands: GLY.9 12 PLIP interactions: 9 interactions with chain A, 3 Ligand-Ligand interactions Hydrogen bonds: A:S.68, A:S.68, G.9, G.9 Water bridges: A:K.27, A:S.28, A:D.69, G.9 Salt bridges: A:K.27, A:K.27, A:H.174, A:R.178

1 x GLY: GLYCINE(Non-covalent)

GLY.9: 6 residues within 4Å: Chain A: S.28, N.31, G.65, W.66, S.67 Ligands: DGL.8 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.28, A:S.28, A:G.65 Water bridges: A:N.31, A:G.65, A:S.67, 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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