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

SDCBP PanDDA analysis group deposition -- The PDZ domans of SDCBP in complex with Z32367954

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.11 Å

Oligo State

monomer

Ligands

2 x UXA: ~{N}-cyclopropyl-1,3-benzodioxole-5-carboxamide(Non-covalent)

UXA.1: 7 residues within 4Å: Chain A: Q.141, L.146, Q.150, D.153, I.154, T.157, H.190 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:D.153, A:I.154, A:H.190 Hydrogen bonds: A:Q.141 UXA.2: 4 residues within 4Å: Chain A: D.69, H.72, K.73 Ligands: SO4.7 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:D.69, A:K.73

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

EDO.3: 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:R.50 EDO.4: 5 residues within 4Å: Chain A: I.29, D.30, F.170, I.171, H.174 1 PLIP interactions: 1 interactions with chain A Water bridges: A:D.30

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

SO4.5: 5 residues within 4Å: Chain A: M.98, 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 SO4.6: 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 SO4.7: 2 residues within 4Å: Chain A: H.72 Ligands: UXA.2 4 PLIP interactions: 4 interactions with chain A Water bridges: A:D.69, A:H.72 Salt bridges: A:R.25, A:H.72

1 x ALA: ALANINE(Non-covalent)

ALA.8: 5 residues within 4Å: Chain A: H.105, V.106, G.107, F.108, L.155 8 PLIP interactions: 6 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:F.108, A:L.155 Hydrogen bonds: A:V.106, A:G.107, A:F.108 Salt bridges: A:H.105 Water bridges: A.8, A.8

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

DGL.9: 7 residues within 4Å: Chain A: K.27, S.28, S.67, S.68, H.174, R.178 Ligands: GLY.10 13 PLIP interactions: 10 interactions with chain A, 3 Ligand-Ligand interactions Hydrogen bonds: A:S.28, A:S.68, A:S.68, G.10, G.10 Water bridges: A:K.27, A:S.28, A:D.69, G.10 Salt bridges: A:K.27, A:K.27, A:H.174, A:R.178

1 x GLY: GLYCINE(Non-covalent)

GLY.10: 5 residues within 4Å: Chain A: S.28, N.31, G.65, S.67 Ligands: DGL.9 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.28, A:N.31, A:N.31, A:G.65 Water bridges: A:N.31, 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

Related Entries With Identical Sequence