SMTL ID : 7ft3.4 (3 other biounits)

SDCBP PanDDA analysis group deposition -- The PDZ domans of SDCBP in complex with Z291279160

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.05 Å

Oligo State

monomer

Ligands

1 x LV4: 1-[2-(trifluoromethyloxy)phenyl]thiourea(Non-covalent)

LV4.1: 5 residues within 4Å: Chain A: S.117, I.118, V.119, K.120, A.125 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.120 Hydrogen bonds: A:I.118 Water bridges: A:K.120

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: 5 residues within 4Å: Chain A: I.29, D.30, F.170, I.171, H.174 No protein-ligand interaction detected (PLIP)

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

SO4.4: 5 residues within 4Å: Chain A: M.98, H.99, S.123, R.126, N.127 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:H.99, A:S.123, A:N.127 Salt bridges: A:H.99, A:R.126 SO4.5: 3 residues within 4Å: Chain A: N.112, K.147, D.148 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.112, A:N.112, A:D.148, A:D.148 Water bridges: A:D.148, A:D.148, A:S.149 SO4.6: 2 residues within 4Å: Chain A: R.25, H.72 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.25, A:H.72

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.110, A:L.155 Hydrogen bonds: A:V.106, A:G.107, A:F.108 Water bridges: A:H.105, A.7, A.7 Salt bridges: A:H.105

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 11 PLIP interactions: 9 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:S.28, A:S.68, G.9, G.9 Water bridges: A:K.27, A:D.30, A:D.69 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 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:S.28, A:N.31, A:G.65, G.9

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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