SMTL ID : 5lf5.1

Myelin-associated glycoprotein (MAG) deglycosylated full extracellular domain with co-purified ligand

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.80 Å

Oligo State

homo-dimer

Ligands

2 x NAG- FUC: alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)(Non-functional Binders)

NAG-FUC.1: 5 residues within 4Å: Chain A: T.313, N.315, S.331, T.332, Q.333 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.313, A:S.331 NAG-FUC.8: 5 residues within 4Å: Chain B: T.313, N.315, S.331, T.332, Q.333 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.331

2 x NGA- GAL- SIA: N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-galactopyranose(Post Translational Modification)(Non-covalent)

NGA-GAL-SIA.2: 8 residues within 4Å: Chain A: Y.48, P.49, K.50, R.101, Y.107, Q.109, Y.110, T.111 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.48, A:T.111 Salt bridges: A:R.101 NGA-GAL-SIA.9: 8 residues within 4Å: Chain B: Y.48, P.49, K.50, R.101, Y.107, Q.109, Y.110, T.111 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.111 Salt bridges: B:R.101

2 x MAN: alpha-D-mannopyranose(Post Translational Modification)(Non-covalent)

MAN.3: 4 residues within 4Å: Chain A: H.4, W.5, P.30, Y.110 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:H.4, A:W.5, A:W.5 MAN.10: 4 residues within 4Å: Chain B: H.4, W.5, P.30, Y.110 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:W.5, B:W.5

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

NAG.4: 2 residues within 4Å: Chain A: N.82, T.84 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.84 NAG.5: 5 residues within 4Å: Chain A: E.227, N.229, V.232, S.241, L.243 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:V.232 Hydrogen bonds: A:E.227, A:E.227, A:S.241, A:S.241 NAG.6: 1 residues within 4Å: Chain A: N.298 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.298 NAG.7: 1 residues within 4Å: Chain A: N.389 No protein-ligand interaction detected (PLIP) NAG.11: 2 residues within 4Å: Chain B: N.82, T.84 No protein-ligand interaction detected (PLIP) NAG.12: 5 residues within 4Å: Chain B: E.227, N.229, V.232, S.241, L.243 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:V.232 Hydrogen bonds: B:E.227, B:S.241, B:S.241 NAG.13: 1 residues within 4Å: Chain B: N.298 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.298 NAG.14: 1 residues within 4Å: Chain B: N.389 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Myelin-associated glycoprotein

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