SMTL ID : 7ywf.1

Monocot chimeric jacalin JAC1 from Oryza sativa: dirigent domain with bound galactobiose

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-trimer

Ligands

3 x GAL- GAL: beta-D-galactopyranose-(1-4)-beta-D-galactopyranose(Non-covalent)

GAL-GAL.1: 9 residues within 4Å: Chain A: H.32, P.34, Q.41, H.81, W.87, V.112, E.113, M.137, N.145 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.41, A:Q.41 GAL-GAL.2: 9 residues within 4Å: Chain B: H.32, P.34, Q.41, H.81, W.87, V.112, E.113, Q.140, N.145 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.41, B:Q.41 GAL-GAL.3: 8 residues within 4Å: Chain C: H.32, P.34, Q.41, H.81, W.87, V.112, E.113, N.145 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Q.41, C:Q.41

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.4: 2 residues within 4Å: Chain A: Y.76, E.96 No protein-ligand interaction detected (PLIP)

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.5: 3 residues within 4Å: Chain B: P.34, G.36, Q.39 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:G.36, B:Q.39, B:Q.39, B:Q.39

1 x DTU: (2R,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL(Non-covalent)

DTU.6: 4 residues within 4Å: Chain B: A.43, V.44, S.46 Chain C: D.48 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.44

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huwa, N. et al., The Crystal Structure of the Defense Conferring Rice Protein Os JAC1 Reveals a Carbohydrate Binding Site on the Dirigent-like Domain. Biomolecules (2022)

Release Date

2022-05-04

Peptides

Dirigent protein: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Dirigent protein

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