SMTL ID : 9s96.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.31 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: 9 residues within 4Å: Chain A: T.43, S.44, T.91, L.92, N.93, N.96, G.116, 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.4: 6 residues within 4Å: Chain A: N.362, E.386, R.608, E.610 Chain B: D.341, S.344 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.610 NAG-NAG.5: 6 residues within 4Å: Chain A: A.437, A.459, N.460, N.461, N.484, F.615 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 6 residues within 4Å: Chain A: S.508, N.532, R.596, G.597, A.598, 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: 10 residues within 4Å: Chain B: Q.109, S.132, S.133, N.156, S.158, H.159, T.179, D.181, H.205 Ligands: SO4.33 No protein-ligand interaction detected (PLIP) NAG-NAG.14: 7 residues within 4Å: Chain A: D.341, S.344 Chain B: N.362, E.386, R.608, E.610, H.614 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.610 NAG-NAG.15: 8 residues within 4Å: Chain B: N.436, A.437, A.459, N.460, N.461, N.484, F.615, M.617 No protein-ligand interaction detected (PLIP) NAG-NAG.17: 4 residues within 4Å: Chain B: G.572, L.573, M.575, N.638 No protein-ligand interaction detected (PLIP)

1 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.3: 28 residues within 4Å: Chain A: S.209, S.232, S.234, Q.235, N.257, S.259, R.260, Q.281, L.282, 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: SO4.22, SO4.23 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.260, A:R.260

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: 4 residues within 4Å: Chain A: S.534, T.536, N.558, R.596 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.16: 3 residues within 4Å: Chain B: S.534, T.536, N.558 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- 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-(1-6)-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.12: 20 residues within 4Å: Chain B: S.209, S.234, Q.235, N.257, S.259, R.260, Q.281, S.283, V.306, K.406, K.429, E.478, G.629, M.630, M.632 Ligands: MAN-MAN.13, MAN-MAN.13, SO4.26, SO4.33, PGE.34 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.260, B:R.260 Water bridges: B:M.630, B:M.630

1 x MAN- MAN: alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose(Non-covalent)

MAN-MAN.13: 12 residues within 4Å: Chain B: R.260, A.285, H.286, V.306, D.308, S.310, S.330, N.332, Y.357 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.12, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.12, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.12 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:S.330, B:N.332 Water bridges: B:S.330

1 x NAG- NAG- FUC: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-FUC.18: 6 residues within 4Å: Chain B: H.696, S.719, N.720, T.739, A.742, N.743 No protein-ligand interaction detected (PLIP)

2 x 01: Typhasterol

01.19: 21 residues within 4Å: Chain A: I.527, I.550, W.551, V.579, 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, S.714 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:I.527, A:W.551, A:F.584, A:F.586, A:L.601, A:Y.627, A:T.631, A:I.642, A:V.667 Hydrogen bonds: A:M.632, A:S.714 01.27: 20 residues within 4Å: Chain B: I.527, I.550, W.551, V.579, F.584, F.586, R.588, L.601, Y.627, T.631, M.632, Y.633, M.634, I.642, Y.643, Q.666, V.667, G.690, V.691, S.714 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:I.527, B:W.551, B:F.584, B:F.586, B:F.586, B:L.601, B:Y.627, B:T.631, B:V.667, B:V.691 Hydrogen bonds: B:M.632, B:M.632, B:S.714

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

NAG.20: 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:E.226 NAG.21: 6 residues within 4Å: Chain A: S.344, T.345, S.348, K.349, S.370, N.373 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.348, A:N.373 NAG.28: 5 residues within 4Å: Chain B: N.201, S.202, E.226, N.227, L.252 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.252 Hydrogen bonds: B:E.226, B:E.226, B:E.226 NAG.29: 4 residues within 4Å: Chain B: S.508, N.532, S.556, M.617 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.532

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

SO4.22: 3 residues within 4Å: Chain A: Q.235, R.260 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.235 Salt bridges: A:R.260 SO4.23: 5 residues within 4Å: Chain A: H.159, N.184, Q.235 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.3, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN-MAN-MAN.3 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.159, A:N.184 SO4.25: 3 residues within 4Å: Chain A: P.737, T.739, R.740 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.739 Salt bridges: A:R.740 SO4.26: 4 residues within 4Å: Chain B: Q.235, R.260 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.12, PGE.34 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.235, B:R.260 Water bridges: B:N.236, B:R.260 SO4.30: 3 residues within 4Å: Chain B: P.737, T.739, R.740 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.739 Salt bridges: B:R.740 SO4.31: 2 residues within 4Å: Chain B: K.161, R.186 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:K.161, B:R.186 SO4.32: 3 residues within 4Å: Chain B: R.84, N.85, Q.109 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.85, B:Q.109 Salt bridges: B:R.84 SO4.33: 6 residues within 4Å: Chain B: H.159, N.184, Q.235 Ligands: NAG-NAG.11, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.12, NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.12 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.184

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.24: 7 residues within 4Å: Chain A: N.261, S.262, H.286, N.287, L.288, G.311, N.312 No protein-ligand interaction detected (PLIP) PGE.34: 9 residues within 4Å: Chain B: R.260, N.261, S.262, H.286, N.287, L.288, G.311 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN-MAN-MAN.12, SO4.26 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.286 Water bridges: B:R.260

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

ACT.35: 11 residues within 4Å: Chain B: I.196, A.197, F.199, P.200, N.201, L.203, F.222, G.223, L.224, C.225, E.226 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.199 Hydrogen bonds: B:P.200, B:L.224, B:C.225 Water bridges: B:E.226, B:E.226, B:E.226

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

2025-09-03

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

Related Entries With Identical Sequence