SMTL ID : 4igr.1

Crystal structure of the kainate receptor GluK3 ligand-binding domain in complex with the agonist ZA302

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.65 Å

Oligo State

homo-dimer

Ligands

2 x 3ZA: (4R)-4-{3-[hydroxy(methyl)amino]-3-oxopropyl}-L-glutamic acid(Non-covalent)

3ZA.1: 15 residues within 4Å: Chain A: E.15, F.18, Y.63, P.90, L.91, T.92, R.97, V.139, G.142, A.143, T.144, N.174, E.191, T.194, Y.217 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:Y.63, A:V.139 Hydrogen bonds: A:E.15, A:P.90, A:P.90, A:T.92, A:T.92, A:A.143, A:T.144, A:E.191, A:T.194 Water bridges: A:V.139 Salt bridges: A:R.97 3ZA.6: 15 residues within 4Å: Chain B: E.15, F.18, Y.63, P.90, L.91, T.92, R.97, V.139, G.142, A.143, T.144, N.174, E.191, T.194, Y.217 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:Y.63, B:V.139 Hydrogen bonds: B:P.90, B:P.90, B:T.92, B:A.143, B:T.144, B:T.144, B:E.191 Water bridges: B:V.139, B:E.191 Salt bridges: B:R.97

4 x K: POTASSIUM ION(Non-covalent)

K.2: 2 residues within 4Å: Chain A: N.5, S.52 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:S.52 K.3: 2 residues within 4Å: Chain A: S.24, R.26 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:R.26 K.7: 2 residues within 4Å: Chain B: N.5, S.52 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:S.52 K.8: 2 residues within 4Å: Chain B: S.24, R.26 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:R.26

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

CL.4: 3 residues within 4Å: Chain A: R.33, R.56, L.57 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain B: R.33, R.56, L.57 Ligand excluded by PLIP

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 4 residues within 4Å: Chain A: T.94, H.95 Chain B: H.95 Ligands: PO4.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.95 Salt bridges: A:H.95 PO4.10: 4 residues within 4Å: Chain A: H.95 Chain B: T.94, H.95 Ligands: PO4.5 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.95 Salt bridges: B:H.95

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Assaf, Z. et al., Chemoenzymatic synthesis of new 2,4-syn-functionalized (S)-glutamate analogues and structure-activity relationship studies at ionotropic glutamate receptors and excitatory amino acid transporters. J.Med.Chem. (2013)

Release Date

2013-03-06

Peptides

Glutamate receptor, ionotropic kainate 3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Glutamate receptor, ionotropic kainate 3

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