SMTL ID : 6zr7.1

X-ray structure of human Dscam Ig7-Ig9

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

1 x NAG- GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-GAL-SIA.1: 8 residues within 4Å: Chain A: Y.111, M.197, I.198, T.199, S.200, Y.201, N.203, D.282 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.199, A:Y.201, A:Y.111, A:Y.111 Water bridges: A:N.203, A:N.203

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

NAG-GAL.2: 7 residues within 4Å: Chain A: I.116, N.118, S.120, L.154, N.156, S.158 Ligands: NAG.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.118, A:N.156, A:S.158, A:S.158 NAG-GAL.3: 2 residues within 4Å: Chain A: D.41, N.74 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.74 Water bridges: A:Q.91

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain A: Q.39, G.42, T.76, E.87, Q.89 Ligands: CA.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.39 Water bridges: A:T.76

1 x CA: CALCIUM ION(Non-covalent)

CA.5: 2 residues within 4Å: Chain A: E.87 Ligands: GOL.4 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.87

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

NAG.6: 3 residues within 4Å: Chain A: Q.107, N.118 Ligands: NAG-GAL.2 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.118

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kozak, S. et al., Homogeneously N-glycosylated proteins derived from the GlycoDelete HEK293 cell line enable diffraction-quality crystallogenesis. Acta Crystallogr D Struct Biol (2020)

Release Date

2020-12-30

Peptides

Down syndrome cell adhesion molecule: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAA

Down syndrome cell adhesion molecule