SMTL ID : 5lfv.2 (1 other biounit)

Crystal structure of glycosylated Myelin-associated glycoprotein (MAG) Ig1-3 with soaked trisaccharide ligand

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.30 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN: 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.1: 6 residues within 4Å: Chain A: S.22, L.75, G.76, N.82, T.84, P.149 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.75, A:P.149

1 x NAG- GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-GAL-SIA.2: 9 residues within 4Å: Chain A: W.5, Y.48, P.49, K.50, R.101, Y.107, Q.109, Y.110, T.111 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:K.50, A:Y.48, A:R.101, A:Q.109, A:Q.109, A:T.111 Hydrophobic interactions: A:W.5 Salt bridges: A:R.101

1 x MAN: alpha-D-mannopyranose(Post Translational Modification)

MAN.3: 4 residues within 4Å: Chain A: H.4, W.5, P.30, Y.110 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:W.5, A:W.5, A:Y.110, A:Y.110

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

NAG.4: 6 residues within 4Å: Chain A: N.229, V.232, V.240, S.241, L.243, Y.272 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.232, A:V.240 Hydrogen bonds: A:N.229, A:S.241 NAG.5: 2 residues within 4Å: Chain A: D.297, N.298 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.297, A:N.298

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

SO4.6: 4 residues within 4Å: Chain A: R.152, G.170, R.171, Q.181 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.171, A:Q.181 Salt bridges: A:R.152 SO4.7: 1 residues within 4Å: Chain A: V.182 No protein-ligand interaction detected (PLIP) SO4.8: 2 residues within 4Å: Chain A: N.229, S.230 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.229, A:S.230, A:S.230 SO4.9: 2 residues within 4Å: Chain A: T.190, R.191 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.191, A:R.191

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pronker, M.F. et al., Structural basis of myelin-associated glycoprotein adhesion and signalling. Nat Commun (2016)

Release Date

2016-12-14

Peptides

Myelin-associated glycoprotein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Myelin-associated glycoprotein

Related Entries With Identical Sequence