SMTL ID : 9s80.1

Crystal structure of the BRL3 ectodomain from Arabidopsis thaliana in complex with brassinolide.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

homo-dimer

Ligands

12 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: 10 residues within 4Å: Chain A: T.43, S.44, T.91, L.92, N.93, N.96, G.116, D.117, S.119, S.120 No protein-ligand interaction detected (PLIP) NAG-NAG.2: 3 residues within 4Å: Chain A: T.89, N.112, S.114 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 3 residues within 4Å: Chain A: N.212, T.214, S.237 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 7 residues within 4Å: Chain A: L.486, S.508, N.532, S.556, R.596, P.616, S.620 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 3 residues within 4Å: Chain A: G.572, L.573, N.638 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 5 residues within 4Å: Chain A: S.719, N.720, T.739, A.742, N.743 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain B: T.89, N.112, S.114 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain B: N.212, T.214, S.237 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 8 residues within 4Å: Chain B: N.484, S.508, N.532, S.556, R.596, P.616, M.617, S.620 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.616 NAG-NAG.16: 3 residues within 4Å: Chain B: G.572, L.573, N.638 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 5 residues within 4Å: Chain B: N.721, N.722, N.743, N.744, S.745 No protein-ligand interaction detected (PLIP) NAG-NAG.18: 5 residues within 4Å: Chain B: S.719, N.720, T.739, A.742, N.743 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- BMA- MAN- MAN- MAN- MAN- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.4: 27 residues within 4Å: Chain A: S.209, S.232, S.234, Q.235, N.257, S.259, R.260, Q.281, S.283, A.285, H.286, V.306, D.308, S.310, S.330, N.332, Y.357, K.429, S.453, E.478, S.578, K.582, G.629, M.630, M.632 Ligands: 1PE.24, SO4.26 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.260, A:R.260, A:M.630 Water bridges: A:M.630 NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.12: 25 residues within 4Å: Chain B: S.209, S.234, Q.235, N.257, S.259, R.260, Q.281, S.283, A.285, H.286, V.306, D.308, S.310, S.330, N.332, Y.357, K.406, K.429, S.453, E.478, G.629, M.630, M.632 Ligands: 1PE.32, SO4.35 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.260, B:R.260 Water bridges: B:M.630, B:M.630

2 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.5: 8 residues within 4Å: Chain A: N.362, E.386, R.608, E.610 Chain B: D.341, S.344, T.345 Ligands: 1PE.24 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.610 NAG-NAG-BMA.13: 9 residues within 4Å: Chain A: D.341, S.344 Chain B: N.362, E.386, R.608, E.610, E.613, H.614 Ligands: 1PE.32 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.610

2 x NAG- NAG- MAN: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-D-mannopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN.7: 3 residues within 4Å: Chain A: T.536, N.558, R.596 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.15: 3 residues within 4Å: Chain B: T.536, N.558, R.596 No protein-ligand interaction detected (PLIP)

2 x BLD: Brassinolide(Non-covalent)

BLD.19: 21 residues within 4Å: Chain A: I.527, I.550, W.551, F.584, F.586, R.588, L.601, Y.627, M.630, T.631, M.632, Y.633, M.634, I.642, Y.643, Q.666, V.667, G.690, V.691, F.712, S.714 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:I.527, A:W.551, A:F.586, A:L.601, A:T.631, A:V.667, A:V.691 Hydrogen bonds: A:Y.627, A:M.630, A:M.632, A:S.714, A:S.714 Water bridges: A:M.630 Salt bridges: A:R.588 BLD.28: 21 residues within 4Å: Chain B: I.527, I.550, W.551, V.579, F.584, F.586, R.588, L.601, Y.627, M.630, T.631, M.632, M.634, I.642, Y.643, Q.666, V.667, G.690, V.691, F.712, S.714 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:I.527, B:I.550, B:W.551, B:W.551, B:F.584, B:F.584, B:F.586, B:L.601, B:T.631, B:V.667, B:V.691 Hydrogen bonds: B:M.632, B:S.714, B:S.714 Water bridges: B:M.630, B:Q.666 Salt bridges: B:R.588

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

NAG.20: 6 residues within 4Å: Chain A: R.84, N.85, Q.109, G.110, S.132, S.133 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Q.109 Hydrogen bonds: A:R.84 NAG.21: 6 residues within 4Å: Chain A: T.178, N.201, S.202, K.204, E.226, N.227 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.204, A:N.227 NAG.22: 5 residues within 4Å: Chain A: A.459, N.460, N.461, N.484, F.615 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.615 Hydrogen bonds: A:N.461 NAG.23: 4 residues within 4Å: Chain A: D.698, Q.700, N.721, N.722 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.700 NAG.29: 6 residues within 4Å: Chain B: R.84, N.85, Q.109, G.110, S.132, S.133 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.84, B:Q.109, B:S.133 NAG.30: 6 residues within 4Å: Chain B: T.178, N.201, S.202, K.204, E.226, N.227 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.204 NAG.31: 5 residues within 4Å: Chain B: A.459, N.460, N.461, N.484, F.615 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.615 Hydrogen bonds: B:N.461

2 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.24: 15 residues within 4Å: Chain A: N.335, P.359, F.360, D.381, S.383, Q.583, E.605, G.606, I.607, R.608, A.609, E.610 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.4, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.4, NAG-NAG-BMA.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.335, A:D.381, A:G.606, A:A.609 1PE.32: 11 residues within 4Å: Chain B: N.335, F.360, Q.583, E.605, I.607, R.608, A.609, E.610 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.12, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.12, NAG-NAG-BMA.13 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.609, B:E.610, B:E.610 Water bridges: B:D.381

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.25: 9 residues within 4Å: Chain A: S.139, V.142, D.143, K.165, L.166, K.167, S.168, F.187, F.195 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.143, A:K.167, A:S.168, A:S.168 EDO.33: 7 residues within 4Å: Chain B: Y.357, P.359, V.379, D.381, K.406, L.408, E.605 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.381, B:E.605

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

SO4.26: 5 residues within 4Å: Chain A: H.159, N.184, Q.235 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.4, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.159, A:N.184 SO4.35: 5 residues within 4Å: Chain B: H.159, N.184, Q.235 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.12, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.12 2 PLIP interactions: 2 interactions with chain B Water bridges: B:N.184, B:N.184

1 x GLY: GLYCINE(Non-covalent)

GLY.27: 4 residues within 4Å: Chain B: P.754, C.755, S.756, S.757 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:P.754

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

ACT.34: 4 residues within 4Å: Chain B: G.592, P.737, T.739, R.740 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.739, B:T.739 Salt bridges: B:R.740

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Caregnato, A. et al., A mechanistic framework for the recognition of chemically diverse brassinosteroids by BRI1-family receptor kinases. To Be Published

Release Date

2025-09-10

Peptides

Receptor-like protein kinase BRI1-like 3: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Receptor-like protein kinase BRI1-like 3