SMTL ID : 5xfd.1

Serial femtosecond X-ray structure of Agrocybe cylindracea galectin with lactose solved by Se-SAD using XFEL (refined against 60,000 patterns)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-dimer

Ligands

2 x NDG- GAL- FUC- A2G: alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose

NDG-GAL-FUC-A2G.1: 11 residues within 4Å: Chain A: N.57, A.59, H.72, R.76, N.85, R.87, W.93, E.96, R.98, N.150, T.152 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:N.57, A:A.59 Hydrogen bonds: A:N.150, A:R.76, A:N.85, A:R.76, A:R.76, A:R.98 Water bridges: A:N.57, A:T.152, A:N.57, A:N.57, A:E.79, A:E.79, A:E.96 NDG-GAL-FUC-A2G.2: 9 residues within 4Å: Chain B: N.57, A.59, H.72, R.76, N.85, W.93, E.96, R.98, N.150 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:N.57, B:A.59 Hydrogen bonds: B:N.150, B:R.76, B:N.85, B:R.76, B:R.76, B:R.98 Water bridges: B:N.57, B:E.79, B:E.79, B:E.96

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yamashita, K. et al., Experimental phase determination with selenomethionine or mercury-derivatization in serial femtosecond crystallography. IUCrJ (2017)

Release Date

2017-08-30

Peptides

Galactoside-binding lectin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Galactoside-binding lectin

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