SMTL ID : 5x2m.2 (1 other biounit)

Crystal structure of the medaka fish taste receptor T1r2a-T1r3 ligand binding domains in complex with L-glutamine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.21 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

13 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 4 residues within 4Å: Chain A: F.57, E.60, E.61, N.64 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.60, A:E.60 Water bridges: A:N.64 NAG.2: 2 residues within 4Å: Chain A: N.71, K.374 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.374 NAG.3: 2 residues within 4Å: Chain A: L.259, N.260 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.258 NAG.4: 4 residues within 4Å: Chain A: S.40, S.41, K.328, N.330 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.328 Water bridges: A:N.330, A:N.330 NAG.5: 1 residues within 4Å: Chain A: N.391 No protein-ligand interaction detected (PLIP) NAG.6: 5 residues within 4Å: Chain A: N.418, S.419, S.420, N.422, E.424 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.420, A:N.422 Water bridges: A:E.425 NAG.7: 3 residues within 4Å: Chain A: N.440, T.442, K.443 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.442, A:T.442, A:K.443 NAG.10: 4 residues within 4Å: Chain A: Q.35 Chain B: N.114, T.116, D.117 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.35, B:D.117 NAG.11: 4 residues within 4Å: Chain B: L.49, K.51, N.351, L.354 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:L.354 NAG.12: 3 residues within 4Å: Chain B: I.436, N.439, S.441 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:I.436 Hydrogen bonds: B:S.441, B:S.441 NAG.13: 1 residues within 4Å: Chain B: N.412 No protein-ligand interaction detected (PLIP) NAG.14: 2 residues within 4Å: Chain B: N.456, T.458 No protein-ligand interaction detected (PLIP) NAG.15: 3 residues within 4Å: Chain A: L.100 Chain B: S.105, N.106 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.105, B:N.106

2 x GLN: GLUTAMINE(Non-covalent)

GLN.8: 9 residues within 4Å: Chain A: F.121, T.122, S.123, G.144, C.145, S.146, F.194, P.245, G.271 7 PLIP interactions: 6 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:F.121 Hydrogen bonds: A:S.123, A:S.146, A:S.146, A:G.147, Q.8 Water bridges: A:S.146 GLN.16: 7 residues within 4Å: Chain B: Q.129, S.130, S.131, G.152, A.153, T.154, Y.202 6 PLIP interactions: 5 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: B:Q.129, B:S.131, B:T.154, B:T.154, B:T.154, Q.16

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

NA.9: 5 residues within 4Å: Chain A: I.62, N.63, S.65, L.68, L.69 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.68 NA.17: 5 residues within 4Å: Chain B: I.67, N.68, N.70, L.73, L.74 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.70

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

CL.18: 6 residues within 4Å: Chain B: P.26, T.86, P.128, Q.129, S.130, M.133 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nuemket, N. et al., Structural basis for perception of diverse chemical substances by T1r taste receptors. Nat Commun (2017)

Release Date

2017-05-24

Peptides

Taste receptor, type 1, member 2a: A
Taste receptor, type 1, member 3: B
Fab16A Heavy chain: C
Fab16A Light chain: D

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
D

C
J

D
K

Taste receptor, type 1, member 2a

Taste receptor, type 1, member 3

Fab16A Heavy chain

Fab16A Light chain

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