SMTL ID : 6qhj.1

High-resolution crystal structure of calcium- and sodium-bound mouse Olfactomedin-1 beta-propeller domain

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.25 Å

Oligo State

monomer

Ligands

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

NAG.1: 1 residues within 4Å: Chain A: N.65 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.65 Water bridges: A:T.67 NAG.2: 3 residues within 4Å: Chain A: L.31, Y.83, N.84 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.31 Hydrogen bonds: A:N.84 Water bridges: A:Y.83 NAG.3: 5 residues within 4Å: Chain A: Q.149, N.150, T.169, W.170, N.171 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.149, A:N.171 Water bridges: A:N.150, A:N.171 NAG.4: 6 residues within 4Å: Chain A: P.13, V.14, L.248, Y.249, N.250 Ligands: GOL.8 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:V.14, A:L.248 Water bridges: A:N.250

1 x CA: CALCIUM ION(Non-covalent)

CA.5: 8 residues within 4Å: Chain A: Y.124, D.133, M.135, E.181, A.182, F.183, L.229, D.230 6 PLIP interactions: 5 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.133, A:E.181, A:A.182, A:L.229, A:D.230, H2O.2

1 x NA: SODIUM ION(Non-functional Binders)

NA.6: 7 residues within 4Å: Chain A: G.79, Q.80, V.81, D.133, L.134, M.135, D.230 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.80, A:L.134

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 3 residues within 4Å: Chain A: K.109, T.110, R.111 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.110, A:T.110 Water bridges: A:T.110 GOL.8: 6 residues within 4Å: Chain A: V.14, V.16, M.57, M.61, L.248 Ligands: NAG.4 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pronker, M.F. et al., Design and structural characterisation of olfactomedin-1 variants as tools for functional studies. BMC Mol Cell Biol (2019)

Release Date

2019-09-11

Peptides

Noelin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Noelin