SMTL ID : 4igt.1

Crystal structure of the GluA2 ligand-binding domain (S1S2J) in complex with the agonist ZA302 at 1.24A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.24 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.13, Y.16, Y.61, P.89, L.90, T.91, R.96, L.138, G.141, S.142, T.143, T.174, E.193, M.196, Y.220 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.61, A:Y.61, A:L.138 Hydrogen bonds: A:Y.61, A:P.89, A:T.91, A:S.142, A:T.143, A:T.174, A:E.193 Water bridges: A:E.193 Salt bridges: A:R.96 3ZA.10: 15 residues within 4Å: Chain B: E.13, Y.16, Y.61, P.89, L.90, T.91, R.96, L.138, G.141, S.142, T.143, T.174, E.193, M.196, Y.220 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:Y.61, B:Y.61, B:L.138 Hydrogen bonds: B:Y.61, B:P.89, B:T.91, B:S.142, B:T.143, B:T.174, B:E.193 Water bridges: B:E.193 Salt bridges: B:R.96

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

SO4.2: 3 residues within 4Å: Chain A: H.46, K.240, Q.244 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.244 Water bridges: A:H.46 Salt bridges: A:H.46, A:K.240 SO4.3: 5 residues within 4Å: Chain A: K.117, E.201, Q.202, C.206, C.261 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.202, A:Q.202 Water bridges: A:K.117, A:K.117 Salt bridges: A:K.117 SO4.4: 4 residues within 4Å: Chain A: K.60, A.63, N.72, S.140 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.72, A:S.140 Water bridges: A:G.62, A:G.141, A:K.144, A:K.144 Salt bridges: A:K.60 SO4.11: 3 residues within 4Å: Chain B: H.46, K.240, Q.244 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.244 Water bridges: B:H.46 Salt bridges: B:H.46, B:K.240 SO4.12: 5 residues within 4Å: Chain B: K.117, E.201, Q.202, C.206, C.261 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.202, B:Q.202 Water bridges: B:K.117, B:K.117 Salt bridges: B:K.117 SO4.13: 4 residues within 4Å: Chain B: K.60, A.63, N.72, S.140 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.72, B:S.140 Water bridges: B:G.62, B:G.141, B:K.144, B:K.144 Salt bridges: B:K.60

2 x LI: LITHIUM ION(Non-covalent)

LI.5: 3 residues within 4Å: Chain A: E.97, I.100, D.101 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.97, A:E.97, A:I.100, H2O.3 LI.14: 3 residues within 4Å: Chain B: E.97, I.100, D.101 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:E.97, B:E.97, B:I.100, H2O.16

8 x GOL: GLYCEROL(Non-functional Binders)

GOL.6: 3 residues within 4Å: Chain A: V.79, V.99, K.226 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.99 Water bridges: A:K.226 GOL.7: 4 residues within 4Å: Chain A: K.116, K.185, G.186 Ligands: GOL.8 No protein-ligand interaction detected (PLIP) GOL.8: 3 residues within 4Å: Chain A: K.116, K.185 Ligands: GOL.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.116, A:K.116 GOL.9: 8 residues within 4Å: Chain A: S.108, L.109, S.194, T.195, E.198, K.210, N.214, K.251 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:G.110, A:S.194, A:E.198, A:K.210, A:K.210, A:N.214, A:K.251 GOL.15: 3 residues within 4Å: Chain B: V.79, V.99, K.226 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.99 Water bridges: B:K.226 GOL.16: 4 residues within 4Å: Chain B: K.116, K.185, G.186 Ligands: GOL.17 No protein-ligand interaction detected (PLIP) GOL.17: 3 residues within 4Å: Chain B: K.116, K.185 Ligands: GOL.16 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.116, B:K.116 GOL.18: 8 residues within 4Å: Chain B: S.108, L.109, S.194, T.195, E.198, K.210, N.214, K.251 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:G.110, B:S.194, B:E.198, B:K.210, B:K.210, B:N.214, B:K.251

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 2: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Glutamate receptor 2

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