SMTL ID : 5mfw.1

Crystal structure of the GluK1 ligand-binding domain in complex with kainate and BPAM-121 at 2.10 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-dimer

Ligands

2 x 7M6: 7-chloro-4-(2-fluoroethyl)-2,3-dihydro-1,2,4-benzothiadiazine 1,1-dioxide(Non-covalent)

7M6.1: 15 residues within 4Å: Chain A: K.103, P.104, F.105, M.106, T.107, L.235, Q.238 Chain B: I.91, P.104, M.106, T.107, S.213, K.214, G.215 Ligands: 7M6.9 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:T.107, B:P.104 Halogen bonds: B:M.106 7M6.9: 15 residues within 4Å: Chain A: I.91, P.104, M.106, T.107, S.213, K.214, G.215 Chain B: K.103, P.104, F.105, M.106, T.107, L.235, Q.238 Ligands: 7M6.1 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:P.104, B:T.107 Hydrogen bonds: A:G.215 Halogen bonds: A:M.106

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

CL.2: 4 residues within 4Å: Chain A: K.103 Chain B: F.101, K.103, R.227 Ligand excluded by PLIP

2 x KAI: 3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE(Non-covalent)

KAI.3: 13 residues within 4Å: Chain A: E.13, Y.61, P.88, L.89, T.90, R.95, V.137, G.140, S.141, T.142, S.173, E.190 Ligands: GOL.7 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.61, A:V.137 Hydrogen bonds: A:P.88, A:T.90, A:T.90, A:S.141, A:T.142, A:T.142, A:E.190, A:E.190 Water bridges: A:V.137, A:V.137, A:V.137 Salt bridges: A:R.95 KAI.10: 13 residues within 4Å: Chain B: E.13, Y.61, P.88, L.89, T.90, R.95, V.137, G.140, S.141, T.142, S.173, E.190, Y.216 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:Y.61, B:V.137 Hydrogen bonds: B:T.90, B:S.141, B:T.142, B:T.142, B:E.190, B:E.190 Water bridges: B:V.137, B:M.143, B:E.190 Salt bridges: B:R.95

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

SO4.4: 2 residues within 4Å: Chain A: R.20, S.22 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.22 Water bridges: A:D.23, A:D.23 Salt bridges: A:R.20 SO4.5: 2 residues within 4Å: Chain A: R.31, K.54 6 PLIP interactions: 6 interactions with chain A Water bridges: A:R.31, A:R.31, A:R.31, A:R.31 Salt bridges: A:R.31, A:K.54 SO4.6: 1 residues within 4Å: Chain A: D.23 No protein-ligand interaction detected (PLIP) SO4.11: 3 residues within 4Å: Chain B: R.31, K.54, L.55 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:L.55 Water bridges: B:R.31, B:R.31, B:R.31 Salt bridges: B:R.31, B:K.54 SO4.12: 3 residues within 4Å: Chain B: R.20, S.22, K.24 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.22 Water bridges: B:R.20 Salt bridges: B:R.20, B:K.24

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 10 residues within 4Å: Chain A: K.60, Y.61, G.62, A.63, N.71, V.137, R.138, D.139, G.140 Ligands: KAI.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.61, A:G.62, A:G.62, A:K.171 Water bridges: A:G.59, A:N.71 GOL.13: 9 residues within 4Å: Chain B: K.60, Y.61, G.62, A.63, N.71, V.137, R.138, D.139, G.140 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.61, B:G.62, B:G.62, B:R.138

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

ACT.8: 2 residues within 4Å: Chain A: K.60, K.171 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.171 Salt bridges: A:K.60

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Larsen, A.P. et al., Identification and Structure-Function Study of Positive Allosteric Modulators of Kainate Receptors. Mol. Pharmacol. (2017)

Release Date

2017-04-12

Peptides

Glutamate receptor ionotropic, kainate 1,Glutamate receptor ionotropic, kainate 1: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Glutamate receptor ionotropic, kainate 1,Glutamate receptor ionotropic, kainate 1

Related Entries With Identical Sequence