SMTL ID : 4gvc.1

Crystal Structure of T-cell Lymphoma Invasion and Metastasis-1 PDZ in complex with phosphorylated Syndecan1 Peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.54 Å

Oligo State

monomer

Ligands

1 x THR- LYS- GLN- GLU- GLU- PHE- PTR- ALA: Syndecan-1(Non-covalent)

THR-LYS-GLN-GLU-GLU-PHE-PTR-ALA.1: 19 residues within 4Å: Chain A: T.21, Y.22, G.23, F.24, S.25, L.26, S.27, S.28, V.29, R.35, N.40, K.43, S.72, K.76, L.79 Ligands: CL.2, ANS.3, CL.4, NA.5 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:K.76, A:L.79, A:L.79 Hydrogen bonds: A:T.21, A:T.21, A:Y.22, A:G.23, A:F.24, A:F.24, A:L.26, A:L.26, A:S.28, A:S.28, A:S.28, A:S.28, A:N.40, A:N.40 Water bridges: A:D.20, A:E.30, A:E.30, A:E.30, A:K.43, A:S.72 Salt bridges: A:K.43

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.2: 3 residues within 4Å: Chain A: S.41, K.43 Ligands: THR-LYS-GLN-GLU-GLU-PHE-PTR-ALA.1 Ligand excluded by PLIP CL.4: 4 residues within 4Å: Ligands: THR-LYS-GLN-GLU-GLU-PHE-PTR-ALA.1, THR-LYS-GLN-GLU-GLU-PHE-PTR-ALA.1, ANS.3, NA.5 Ligand excluded by PLIP

1 x ANS: 5-(DIMETHYLAMINO)-1-NAPHTHALENESULFONIC ACID(DANSYL ACID)(Non-covalent)

ANS.3: 6 residues within 4Å: Chain A: V.29, Y.38 Ligands: THR-LYS-GLN-GLU-GLU-PHE-PTR-ALA.1, THR-LYS-GLN-GLU-GLU-PHE-PTR-ALA.1, CL.4, NA.5 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.29

1 x NA: SODIUM ION(Non-functional Binders)

NA.5: 3 residues within 4Å: Ligands: THR-LYS-GLN-GLU-GLU-PHE-PTR-ALA.1, ANS.3, CL.4 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, X. et al., The structure of the Tiam1 PDZ domain/ phospho-syndecan1 complex reveals a ligand conformation that modulates protein dynamics. Structure (2013)

Release Date

2013-03-13

Peptides

T-lymphoma invasion and metastasis-inducing protein 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

T-lymphoma invasion and metastasis-inducing protein 1

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