SMTL ID : 6qm3.1

Crystal structure of a calcium- and sodium-bound mouse Olfactomedin-1 disulfide-linked dimer of the Olfactomedin domain and part of coiled coil

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

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

NAG.1: 2 residues within 4Å: Chain A: T.76, N.78 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:T.76 NAG.2: 4 residues within 4Å: Chain A: E.6, L.44, Y.96, N.97 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.44 Hydrogen bonds: A:E.6, A:N.97 NAG.3: 3 residues within 4Å: Chain A: Q.162, T.182, N.184 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.162, A:N.184 NAG.4: 4 residues within 4Å: Chain A: S.24, V.27, L.261, N.263 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:V.27, A:L.261 Hydrogen bonds: A:S.24, A:N.263 NAG.10: 3 residues within 4Å: Chain B: T.76, D.77, N.78 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.78 NAG.11: 2 residues within 4Å: Chain B: L.44, N.97 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.44 Hydrogen bonds: B:N.97 NAG.12: 3 residues within 4Å: Chain B: Q.162, T.182, N.184 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.162, B:N.184 Water bridges: B:N.184 NAG.13: 4 residues within 4Å: Chain B: S.24, V.27, L.261, N.263 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:V.27 Hydrogen bonds: B:S.24

1 x CAC: CACODYLATE ION(Non-covalent)

CAC.5: 6 residues within 4Å: Chain A: F.36, Y.58, W.139, G.140, G.141 Ligands: ACT.9 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.58, A:Y.58, A:N.133, A:G.141

2 x CA: CALCIUM ION(Non-covalent)

CA.6: 5 residues within 4Å: Chain A: D.146, E.194, A.195, L.242, D.243 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.146, A:E.194, A:A.195, A:L.242, H2O.1 CA.14: 6 residues within 4Å: Chain B: D.146, M.148, E.194, A.195, L.242, D.243 5 PLIP interactions: 4 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.146, B:E.194, B:A.195, B:L.242, H2O.4

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

NA.7: 5 residues within 4Å: Chain A: G.92, Q.93, D.146, L.147, D.243 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.93 NA.15: 5 residues within 4Å: Chain B: G.92, Q.93, D.146, L.147, D.243 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.147, B:D.243

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.8: 4 residues within 4Å: Chain A: S.34, G.57, Y.58, H.59 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.58, A:H.59, A:H.59 ACT.9: 5 residues within 4Å: Chain A: A.138, W.139, G.140, Y.208 Ligands: CAC.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.208 ACT.16: 4 residues within 4Å: Chain B: S.186, Y.187, Y.216, Y.227 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.187, B:Y.227

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: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Noelin