SMTL ID : 8blv.1 (1 other biounit)

The PDZ domains of human SDCBP with a bound SDC4 C-terminal peptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

1 x ALA- PRO- THR- ASN- GLU- PHE- TYR- ALA: Syndecan-4(Non-covalent)

ALA-PRO-THR-ASN-GLU-PHE-TYR-ALA.1: 12 residues within 4Å: Chain A: H.105, V.106, G.107, F.108, I.109, F.110, K.111, T.116, V.119, D.148, L.155 Ligands: EDO.4 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:H.105, A:F.108, A:I.109, A:F.110, A:V.119, A:D.148, A:L.155 Hydrogen bonds: A:V.106, A:G.107, A:F.108, A:F.108, A:F.108, A:F.110, A:F.110, A:K.111, A:T.116 Water bridges: A:K.111 Salt bridges: A:H.105

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

SO4.2: 4 residues within 4Å: Chain A: H.99, S.123, R.126, N.127 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.123, A:N.127 Water bridges: A:R.126 Salt bridges: A:H.99, A:R.126 SO4.3: 3 residues within 4Å: Chain A: N.139, S.158, G.159 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.139, A:G.159 Water bridges: A:S.158

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

EDO.4: 4 residues within 4Å: Chain A: D.101, T.103, H.105 Ligands: ALA-PRO-THR-ASN-GLU-PHE-TYR-ALA.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.103, A:H.105 EDO.5: 5 residues within 4Å: Chain A: Q.36, L.37, V.38, F.51, N.142 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.38, A:N.142 Water bridges: A:F.51

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bradshaw, W.J. et al., The PDZ domains of human SDCBP with a bound SDC4 C-terminal peptide. To Be Published

Release Date

2022-12-21

Peptides

Syntenin-1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Syntenin-1

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