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

SDCBP PanDDA analysis group deposition -- The PDZ domans of SDCBP in complex with Z1454310449

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

monomer

Ligands

1 x UQS: N-[(2-fluorophenyl)methyl]-1H-pyrazol-4-amine(Non-covalent)

UQS.1: 10 residues within 4Å: Chain A: N.112, G.113, N.134, I.135, V.143, G.145, L.146, I.151, F.172, M.184 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.134, A:I.135, A:V.143, A:G.145

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

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

SO4.4: 4 residues within 4Å: Chain A: H.99, S.123, R.126, N.127 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:H.99, A:S.123, A:N.127 Water bridges: A:H.99, A:H.99 Salt bridges: A:H.99, A:R.126

1 x ALA: ALANINE(Non-covalent)

ALA.5: 5 residues within 4Å: Chain A: H.105, V.106, G.107, F.108, F.110 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.108, A:F.110 Hydrogen bonds: A:V.106, A:G.107, A:F.108

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

DGL.6: 7 residues within 4Å: Chain A: K.27, S.28, S.67, S.68, H.174, R.178 Ligands: GLY.7 12 PLIP interactions: 3 Ligand-Ligand interactions, 9 interactions with chain A Hydrogen bonds: G.7, G.7, A:S.28, A:S.68 Water bridges: G.7, A:S.28, A:D.30, A:R.178 Salt bridges: A:K.27, A:K.27, A:H.174, A:R.178

1 x GLY: GLYCINE(Non-covalent)

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

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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