SMTL ID : 2id5.1

Crystal Structure of the Lingo-1 Ectodomain

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-tetramer

Ligands

9 x NAG- NAG- MAN: alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN.1: 7 residues within 4Å: Chain A: T.232, H.233, F.252, N.254, S.256, Y.257, Q.278 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.2: 8 residues within 4Å: Chain A: Y.257, Q.278, V.280, N.302, S.304, I.326, R.352, Q.353 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.353 NAG-NAG-MAN.4: 4 residues within 4Å: Chain A: K.203, N.225, T.227, Y.249 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.6: 7 residues within 4Å: Chain B: Q.278, V.280, N.302, S.304, I.326, R.352, Q.353 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.352, B:R.352, B:Q.353 NAG-NAG-MAN.7: 4 residues within 4Å: Chain B: K.203, N.225, T.227, Y.249 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.8: 7 residues within 4Å: Chain C: T.232, H.233, F.252, N.254, S.256, Y.257, Q.278 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.9: 8 residues within 4Å: Chain C: Q.278, V.280, N.302, S.304, I.326, D.328, R.352, Q.353 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:R.352, C:R.352, C:Q.353 NAG-NAG-MAN.10: 4 residues within 4Å: Chain C: K.203, N.225, T.227, Y.249 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN.13: 4 residues within 4Å: Chain D: K.203, N.225, T.227, Y.249 No protein-ligand interaction detected (PLIP)

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

NAG-NAG.3: 3 residues within 4Å: Chain A: P.211, Y.212, N.235 No protein-ligand interaction detected (PLIP) NAG-NAG.12: 7 residues within 4Å: Chain D: Q.278, V.280, N.302, S.304, I.326, R.352, Q.353 No protein-ligand interaction detected (PLIP)

2 x NAG- NAG- MAN- MAN: alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-MAN-MAN.5: 7 residues within 4Å: Chain B: T.232, H.233, F.252, N.254, S.256, Y.257, Q.278 No protein-ligand interaction detected (PLIP) NAG-NAG-MAN-MAN.11: 9 residues within 4Å: Chain D: R.88, T.232, H.233, F.252, N.254, S.256, Y.257, E.276, Q.278 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.88

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

NAG.14: 6 residues within 4Å: Chain A: F.80, N.81, S.104, N.105, N.129 Chain B: R.347 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:S.104, B:R.347 NAG.15: 4 residues within 4Å: Chain A: N.138, D.139, N.163, N.187 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.139, A:N.187, A:N.187 Water bridges: A:N.163 NAG.16: 6 residues within 4Å: Chain A: N.453, G.454, T.455, H.472, L.473, H.474 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.453, A:T.455, A:H.472, A:H.474 NAG.17: 5 residues within 4Å: Chain B: E.59, F.80, N.81, R.83, N.105 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.83 NAG.18: 3 residues within 4Å: Chain B: N.138, N.163, N.187 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.187, B:N.187 NAG.19: 3 residues within 4Å: Chain B: P.211, Y.212, N.235 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.235, B:N.235 NAG.20: 4 residues within 4Å: Chain B: N.453, G.454, L.473, H.474 No protein-ligand interaction detected (PLIP) NAG.21: 6 residues within 4Å: Chain C: F.80, N.81, S.104, N.105, N.129 Chain D: R.347 5 PLIP interactions: 2 interactions with chain C, 3 interactions with chain D Hydrogen bonds: C:S.104, C:N.129, D:R.347, D:R.347, D:R.347 NAG.22: 3 residues within 4Å: Chain C: N.138, N.163, N.187 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:N.163, C:N.187 NAG.23: 3 residues within 4Å: Chain C: P.211, Y.212, N.235 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.212 NAG.24: 4 residues within 4Å: Chain C: N.453, G.454, L.473, H.474 No protein-ligand interaction detected (PLIP) NAG.25: 3 residues within 4Å: Chain D: P.211, Y.212, N.235 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:Y.212 Hydrogen bonds: D:N.235 NAG.26: 5 residues within 4Å: Chain D: N.453, G.454, H.472, L.473, H.474 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:N.453, D:G.454, D:G.454

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mosyak, L. et al., The structure of the Lingo-1 ectodomain, a module implicated in central nervous system repair inhibition. J.Biol.Chem. (2006)

Release Date

2006-09-26

Peptides

Leucine rich repeat neuronal 6A: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Leucine rich repeat neuronal 6A