SMTL ID : 5x2q.2 (1 other biounit)

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

hetero-1-1-1-1-mer

Ligands

1 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.1: 6 residues within 4Å: Chain A: R.33, Q.35 Chain B: N.114, T.116, D.117, W.400 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.33

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

NAG.2: 4 residues within 4Å: Chain A: F.57, E.60, E.61, N.64 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.60, A:E.60 NAG.3: 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.4: 2 residues within 4Å: Chain A: N.391, T.393 No protein-ligand interaction detected (PLIP) NAG.5: 5 residues within 4Å: Chain A: N.418, S.419, S.420, N.422, E.424 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.420, A:S.420 NAG.6: 3 residues within 4Å: Chain A: N.440, T.442, K.443 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:N.440 NAG.7: 2 residues within 4Å: Chain A: L.395, N.396 No protein-ligand interaction detected (PLIP) NAG.12: 4 residues within 4Å: Chain B: L.49, K.51, A.350, N.351 No protein-ligand interaction detected (PLIP) NAG.13: 2 residues within 4Å: Chain B: N.439, S.441 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.441, B:S.441 NAG.14: 2 residues within 4Å: Chain B: N.412, S.417 1 PLIP interactions: 1 interactions with chain B Water bridges: B:N.412

2 x GLY: GLYCINE(Non-covalent)

GLY.8: 7 residues within 4Å: Chain A: F.121, T.122, S.123, G.144, C.145, S.146, F.194 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.123, A:G.144, A:S.146 Water bridges: A:F.194 GLY.15: 7 residues within 4Å: Chain B: S.130, S.131, G.152, A.153, T.154, Y.202, L.257 6 PLIP interactions: 5 interactions with chain B, 1 Ligand-Ligand interactions Hydrogen bonds: B:S.131, B:G.152, B:T.154, B:T.154, G.15 Water bridges: B:E.132

3 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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.65, A:L.68 NA.11: 5 residues within 4Å: Chain A: F.150, E.153, Y.156, F.159, N.404 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.159 NA.16: 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:L.73

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

CL.10: 3 residues within 4Å: Chain A: K.246, N.275, K.276 Ligand excluded by PLIP CL.17: 6 residues within 4Å: Chain B: P.26, T.86, P.128, Q.129, S.130, M.133 Ligand excluded by PLIP

1 x CA: CALCIUM ION(Non-covalent)

CA.18: 1 residues within 4Å: Chain D: D.1 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:D.1

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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