SMTL ID : 1w9e.1

Crystal structure of the PDZ tandem of human syntenin in complex with TNEFYF peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.56 Å

Oligo State

homo-dimer

Ligands

3 x GLU- PHE- TYR- PHE: TNEFYF PEPTIDE(Non-covalent)

GLU-PHE-TYR-PHE.1: 8 residues within 4Å: Chain A: K.17, I.18, G.19, L.20, R.21, Q.35, H.68, L.71 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Q.35, A:H.68, A:L.71 Hydrogen bonds: A:I.18, A:G.19, A:L.20, A:L.20, A:L.20, A:R.21 Water bridges: A:K.17, A:K.17 Salt bridges: A:K.17, A:K.17 pi-Cation interactions: A:K.17 GLU-PHE-TYR-PHE.2: 13 residues within 4Å: Chain B: H.101, V.102, G.103, F.104, I.105, F.106, K.107, V.115, D.144, S.145, I.147, A.148, L.151 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:H.101, B:F.104, B:F.104, B:I.105, B:F.106, B:F.106, B:V.115, B:D.144, B:I.147, B:A.148, B:L.151 Hydrogen bonds: B:V.102, B:G.103, B:F.104, B:F.104, B:F.104, B:F.106, B:F.106 Water bridges: B:D.97, B:D.97, B:T.99, B:H.101, B:T.112, B:D.144 Salt bridges: B:H.101 pi-Stacking: B:H.101 GLU-PHE-TYR-PHE.3: 11 residues within 4Å: Chain A: H.101, V.102, G.103, F.104, I.105, F.106, K.107, V.115, D.144, A.148, L.151 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:H.101, A:F.104, A:F.104, A:I.105, A:F.106, A:F.106, A:V.115, A:D.144, A:A.148, A:A.148, A:L.151 Hydrogen bonds: A:V.102, A:G.103, A:F.104, A:F.104, A:F.104, A:F.106, A:F.106 Water bridges: A:D.97, A:D.97, A:D.97, A:H.101, A:D.144 Salt bridges: A:H.101 pi-Stacking: A:H.101

1 x BEZ: BENZOIC ACID(Non-covalent)

BEZ.4: 4 residues within 4Å: Chain A: H.95, S.119, R.122, N.123 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:H.95 Hydrogen bonds: A:H.95, A:N.123 Water bridges: A:R.122 Salt bridges: A:H.95, A:R.122 pi-Stacking: A:H.95

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Grembecka, J. et al., The Binding of the Pdz Tandem of Syntenin to Target Proteins. Biochemistry (2006)

Release Date

2006-03-22

Peptides

SYNTENIN 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

SYNTENIN 1

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