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

SDCBP PanDDA analysis group deposition -- The PDZ domans of SDCBP in complex with Z198195770

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

1 x LJA: N-[3-(carbamoylamino)phenyl]acetamide(Non-covalent)

LJA.1: 7 residues within 4Å: Chain A: F.108, I.109, F.110, D.148, S.149, A.152 Ligands: GLY.9 7 PLIP interactions: 5 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:F.110, A:D.148 Hydrogen bonds: A:F.108, A:F.110, A:S.149, G.9 Water bridges: G.9

3 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:E.137 EDO.3: 4 residues within 4Å: Chain A: D.30, F.170, I.171, H.174 5 PLIP interactions: 5 interactions with chain A Water bridges: A:D.30, A:D.30, A:D.30, A:D.30, A:H.174 EDO.4: 3 residues within 4Å: Chain A: S.45, L.46, G.48 No protein-ligand interaction detected (PLIP)

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

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

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

DGL.7: 7 residues within 4Å: Chain A: K.27, S.28, S.67, S.68, H.174, R.178 Ligands: GLY.8 11 PLIP interactions: 9 interactions with chain A, 2 Ligand-Ligand interactions Hydrogen bonds: A:S.28, A:S.68, A:S.68, G.8, G.8 Water bridges: A:K.27, A:R.178 Salt bridges: A:K.27, A:K.27, A:H.174, A:R.178

2 x GLY: GLYCINE(Non-covalent)

GLY.8: 5 residues within 4Å: Chain A: S.28, N.31, G.65, S.67 Ligands: DGL.7 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Ligand interactions Hydrogen bonds: A:S.28, A:G.65, A:G.65, G.8 Water bridges: A:N.31, A:G.65 GLY.9: 5 residues within 4Å: Chain A: H.105, V.106, G.107, F.108 Ligands: LJA.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.106, A:G.107, A:F.108 Salt bridges: A:H.105

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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