SMTL ID : 9s8z.1

Crystal structure of the BRI1 ectodomain from Arabidopsis thaliana in complex with 28-homobrassinolide.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN: alpha-D-mannopyranose-(1-3)-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.1: 11 residues within 4Å: Chain A: S.107, S.130, R.131, F.152, N.154, S.156, S.157, V.177, D.179, H.204 Ligands: NAG-NAG-BMA-MAN-MAN-MAN-MAN.3 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.2: 4 residues within 4Å: Chain A: S.186, K.211, N.233, S.235 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 4 residues within 4Å: Chain A: N.351, S.353, E.376 Ligands: NAG.14 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 7 residues within 4Å: Chain A: M.605, N.636, T.638, S.639, R.640 Ligands: NAG-NAG-BMA-MAN-MAN.5, NAG-NAG-BMA-MAN-MAN.5 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]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.3: 18 residues within 4Å: Chain A: S.230, H.249, D.251, S.253, G.254, L.273, N.275, S.277, S.278, Y.295, E.300, A.593, G.594, K.595, H.645, S.647 Ligands: NAG-NAG-BMA-MAN.1, NAG-NAG-BMA-MAN.1 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-3)-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.5: 16 residues within 4Å: Chain A: N.521, N.545, T.569, D.603, M.605, K.606, E.608, H.610, S.630, T.631, R.632, N.633, P.634, C.635, N.636 Ligands: NAG-NAG.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.603, A:P.634

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.6: 5 residues within 4Å: Chain A: S.549, G.550, N.551, N.573, G.574 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.573

1 x 01: 28-homobrassinolide

01.8: 19 residues within 4Å: Chain A: I.540, I.563, W.564, Y.597, Y.599, K.601, L.615, Y.642, H.645, T.646, S.647, P.648, T.649, M.657, F.681, I.682, N.705, I.706, T.729 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:W.564, A:W.564, A:Y.597, A:Y.599, A:Y.599, A:L.615, A:Y.642, A:F.681, A:F.681, A:I.682, A:I.706 Hydrogen bonds: A:Y.597, A:H.645, A:S.647, A:T.729, A:T.729 Salt bridges: A:K.601

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

SO4.9: 3 residues within 4Å: Chain A: S.31, Y.33, R.34 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.34 SO4.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) SO4.11: 4 residues within 4Å: Chain A: R.596, Q.619, G.620, H.645 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.596, A:H.645

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

NA.12: 7 residues within 4Å: Chain A: T.455, I.456, E.477, E.479, I.480, P.481, L.500 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.456, A:I.456

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

NAG.13: 3 residues within 4Å: Chain A: N.85, N.112, G.113 No protein-ligand interaction detected (PLIP) NAG.14: 5 residues within 4Å: Chain A: E.376, N.401, R.622, Q.625 Ligands: NAG-NAG.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.401, A:Q.625 NAG.15: 5 residues within 4Å: Chain A: M.485, Y.486, K.488, N.510, R.534 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:Y.486 Hydrogen bonds: A:K.488, A:N.510, A:R.534

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.16: 7 residues within 4Å: Chain A: I.40, K.43, D.44, K.49, W.55, S.56, S.57 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.43, A:D.44 Water bridges: A:S.57

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

ACT.17: 8 residues within 4Å: Chain A: S.258, G.259, D.260, F.261, F.281, V.282, P.286, F.303 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.282

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

EDO.18: 7 residues within 4Å: Chain A: F.374, F.618, I.621, R.622, S.623, E.624 Ligands: EDO.19 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.623, A:S.623 EDO.19: 6 residues within 4Å: Chain A: V.598, S.623, V.641, Y.642, G.643 Ligands: EDO.18 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.623

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

Protein BRASSINOSTEROID INSENSITIVE 1: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Protein BRASSINOSTEROID INSENSITIVE 1

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