SMTL ID : 6rlc.1 (1 other biounit)

Crystal structure of the PDZ tandem of syntenin in complex with fragment F13

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x K7Z: (2~{S})-2-[3-(4-chlorophenyl)sulfanylpropanoylamino]-3-methyl-butanoic acid(Non-covalent)

K7Z.1: 10 residues within 4Å: Chain A: H.101, V.102, G.103, F.104, I.105, F.106, D.144, S.145, A.148, L.151 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.104, A:D.144, A:A.148, A:L.151 Hydrogen bonds: A:G.100, A:V.102, A:G.103, A:F.104, A:F.104 Salt bridges: A:H.101 K7Z.3: 10 residues within 4Å: Chain B: H.101, V.102, G.103, F.104, I.105, F.106, D.144, S.145, A.148, L.151 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:F.104, B:I.105, B:D.144, B:A.148, B:L.151 Hydrogen bonds: B:V.102, B:G.103, B:F.104, B:F.104, B:F.104 Salt bridges: B:H.101

2 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 4 residues within 4Å: Chain A: K.17, I.18, G.19, L.20 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.18, A:G.19 Salt bridges: A:K.17 ACT.4: 6 residues within 4Å: Chain B: K.17, I.18, G.19, L.20, R.21, K.72 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:I.18, B:G.19, B:L.20, B:L.20 Salt bridges: B:K.72

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Leblanc, R. et al., Pharmacological inhibition of syntenin PDZ2 domain impairs breast cancer cell activities and exosome loadifing with syndecan and EpCAM cargo. J Extracell Vesicles (2020)

Release Date

2021-02-03

Peptides

Syntenin-1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Syntenin-1

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