SMTL ID : 8yaa.1

Cryo-EM structure of MIK2-SCOOP12-BAK1

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY 3.34 Å

Oligo State

hetero-1-1-1-mer

Ligands

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-3)-[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.1: 9 residues within 4Å: Chain A: N.12, Q.22, D.25 Chain B: W.320, T.343, V.344, E.367, N.368, N.415 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.12, B:N.415

10 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: 3 residues within 4Å: Chain A: R.133, T.136, N.158 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.133, A:R.133 NAG-NAG.3: 3 residues within 4Å: Chain A: L.100, N.124, N.171 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.171 NAG-NAG.4: 1 residues within 4Å: Chain B: N.170 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain B: E.115, N.137, G.138 No protein-ligand interaction detected (PLIP) NAG-NAG.7: 2 residues within 4Å: Chain B: N.421, N.445 No protein-ligand interaction detected (PLIP) NAG-NAG.8: 2 residues within 4Å: Chain B: E.235, N.281 No protein-ligand interaction detected (PLIP) NAG-NAG.9: 4 residues within 4Å: Chain B: P.196, N.197, K.220, N.221 No protein-ligand interaction detected (PLIP) NAG-NAG.10: 3 residues within 4Å: Chain B: W.457, N.458, N.482 No protein-ligand interaction detected (PLIP) NAG-NAG.11: 3 residues within 4Å: Chain B: G.313, N.338, R.362 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 3 residues within 4Å: Chain B: P.238, E.239, N.242 No protein-ligand interaction detected (PLIP)

1 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.6: 7 residues within 4Å: Chain B: S.516, Y.536, N.538, S.540, R.541, D.562, D.586 No protein-ligand interaction detected (PLIP)

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

NAG.13: 2 residues within 4Å: Chain A: Q.86, N.89 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.86 NAG.14: 2 residues within 4Å: Chain A: S.56, N.78 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.56 NAG.15: 3 residues within 4Å: Chain B: N.566, Q.567, N.591 No protein-ligand interaction detected (PLIP) NAG.16: 4 residues within 4Å: Chain B: N.326, Q.327, N.350, N.351 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Q.327 Hydrogen bonds: B:N.351 NAG.17: 3 residues within 4Å: Chain B: S.183, N.206, N.207 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.207 NAG.18: 3 residues within 4Å: Chain B: T.20, N.21, E.64 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.20, B:T.20, B:N.21 NAG.19: 5 residues within 4Å: Chain B: A.1, A.4, E.8, P.76, N.77 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:A.4 Hydrogen bonds: B:N.77 NAG.20: 4 residues within 4Å: Chain B: R.55, N.57, T.59, D.82 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:D.82 Hydrogen bonds: B:R.55

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Jia, F. et al., N-glycosylation facilitates the activation of a plant cell-surface receptor. Nat.Plants (2024)

Release Date

2024-10-30

Peptides

BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1: A
MDIS1-interacting receptor like kinase 2: B
Serine rich endogenous peptide 12: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
A

C
B

BRASSINOSTEROID INSENSITIVE 1-associated receptor kinase 1

MDIS1-interacting receptor like kinase 2

Serine rich endogenous peptide 12

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