SMTL ID : 5amo.1

Structure of a mouse Olfactomedin-1 disulfide-linked dimer of the Olfactomedin domain and part of the coiled coil

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

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

NAG-NAG.1: 5 residues within 4Å: Chain A: N.197, E.200, L.238, Y.290, N.291 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.197 NAG-NAG.2: 3 residues within 4Å: Chain A: V.221, L.455, N.457 No protein-ligand interaction detected (PLIP) NAG-NAG.3: 4 residues within 4Å: Chain B: N.197, L.238, Y.290, N.291 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.197 NAG-NAG.4: 4 residues within 4Å: Chain B: Q.356, N.357, T.376, N.378 No protein-ligand interaction detected (PLIP)

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

NAG.5: 3 residues within 4Å: Chain A: Q.356, N.357, N.378 No protein-ligand interaction detected (PLIP) NAG.6: 3 residues within 4Å: Chain B: V.221, L.455, N.457 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.221, B:L.455

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 3 residues within 4Å: Chain B: D.271, N.272, F.273 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.272, B:F.273 GOL.8: 5 residues within 4Å: Chain B: S.228, G.251, Y.252, H.253, N.254 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:S.228, B:Y.252, B:H.253, B:H.253, B:N.254 GOL.9: 3 residues within 4Å: Chain B: T.222, K.429, Y.430 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.222, B:Y.430, B:Y.430

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.10: 1 residues within 4Å: Chain B: N.346 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pronker, M.F. et al., Olfactomedin-1 Has a V-Shaped Disulfide-Linked Tetrameric Structure. J.Biol.Chem. (2015)

Release Date

2015-04-29

Peptides

NOELIN: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

NOELIN