SMTL ID : 9gxz.1

Structure of the Medicago truncatula LYR4 ectodomain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

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

NAG.1: 2 residues within 4Å: Chain A: N.37 Ligands: SO4.8 No protein-ligand interaction detected (PLIP) NAG.2: 9 residues within 4Å: Chain A: N.73, N.102, N.115, T.116, S.117 Ligands: NAG.3, NAG.4, NAG.6, SO4.11 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.102 Water bridges: A:N.73, A:N.73, A:T.104, A:H.114 NAG.3: 9 residues within 4Å: Chain A: N.73, S.74, L.78, P.100, I.101, N.102, H.114 Ligands: NAG.2, SO4.11 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:L.78 Hydrogen bonds: A:N.102 Water bridges: A:N.73, A:S.74 NAG.4: 7 residues within 4Å: Chain A: S.106, N.107, Q.113, N.115, Q.147, T.162 Ligands: NAG.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.106, A:Q.113 NAG.5: 4 residues within 4Å: Chain A: F.128, N.132, N.133, F.222 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.128 Hydrogen bonds: A:N.132 Water bridges: A:N.133, A:N.133 NAG.6: 4 residues within 4Å: Chain A: S.117, T.119, N.160 Ligands: NAG.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.117, A:T.119, A:T.119

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

SO4.7: 3 residues within 4Å: Chain A: S.75, A.76, S.77 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.76, A:S.77, A:S.77 Water bridges: A:S.75 SO4.8: 4 residues within 4Å: Chain A: K.28, Y.36, N.37 Ligands: NAG.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.37 Water bridges: A:K.28, A:K.28, A:K.28, A:N.37, A:N.37, A:S.38 Salt bridges: A:K.28 SO4.9: 2 residues within 4Å: Chain A: T.123, R.157 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.123 Water bridges: A:T.123, A:T.123 Salt bridges: A:R.157 SO4.10: 4 residues within 4Å: Chain A: T.59, P.60, Q.61, F.62 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.59, A:Q.61, A:Q.61 SO4.11: 2 residues within 4Å: Ligands: NAG.2, NAG.3 No protein-ligand interaction detected (PLIP)

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

EDO.12: 6 residues within 4Å: Chain A: C.32, T.126, Y.127, F.128, I.145, E.152 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.126, A:F.128, A:E.152, A:E.152 Water bridges: A:Y.127, A:Y.127 EDO.13: 3 residues within 4Å: Chain A: P.234, Q.235, K.236 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.235, A:K.236, A:K.236 EDO.14: 3 residues within 4Å: Chain A: T.64, S.66, S.67 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.64, A:T.64 EDO.15: 6 residues within 4Å: Chain A: V.187, S.188, E.191, I.219, F.220, Y.221 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.191, A:Y.221 Water bridges: A:G.190 EDO.16: 3 residues within 4Å: Chain A: S.214, S.215, T.216 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.215, A:T.216 EDO.17: 7 residues within 4Å: Chain A: C.32, E.33, N.34, T.35, Q.142, I.145 Ligands: EDO.21 No protein-ligand interaction detected (PLIP) EDO.18: 3 residues within 4Å: Chain A: V.238, K.239, H.240 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.239, A:H.240, A:H.240 Water bridges: A:I.237 EDO.19: 2 residues within 4Å: Chain A: N.208, S.215 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Q.205, A:N.208 Water bridges: A:V.193, A:V.193, A:S.215, A:S.217 EDO.20: 3 residues within 4Å: Chain A: H.70, Y.118, T.119 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.119 Water bridges: A:S.117, A:T.119 EDO.21: 4 residues within 4Å: Chain A: E.33, N.34, T.35 Ligands: EDO.17 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.35, A:T.35

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gysel, K. et al., Structural basis for size-selective perception of chitin in plants. To Be Published

Release Date

2025-07-16

Peptides

LysM-domain receptor-like kinase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

LysM-domain receptor-like kinase