SMTL ID : 5epq.1

Structure at 1.75 A resolution of a glycosylated, lipid-binding, lipocalin-like protein

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

monomer

Ligands

2 x NAG- NAG- BMA: beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.1: 6 residues within 4Å: Chain A: N.44, T.46, T.61, Y.63, L.69 Ligands: EDO.6 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 4 residues within 4Å: Chain A: A.71, R.73, N.88, D.89 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:A.71 Water bridges: A:A.71

1 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: 7 residues within 4Å: Chain A: E.132, I.135, K.136, K.139, Y.149, F.152, N.154 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.132, A:I.135, A:K.136

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

NAG.4: 3 residues within 4Å: Chain A: H.52, Y.57, N.75 3 PLIP interactions: 3 interactions with chain A Water bridges: A:G.58, A:V.74, A:N.75

1 x OLA: OLEIC ACID(Non-covalent)

OLA.5: 12 residues within 4Å: Chain A: L.31, V.42, D.62, E.66, Y.67, E.70, H.72, F.85, T.90, Y.93, F.109, L.122 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.31, A:V.42, A:F.85, A:F.85, A:T.90, A:F.109, A:L.122 Hydrogen bonds: A:Y.67

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 5 residues within 4Å: Chain A: Y.30, R.32, T.46 Ligands: NAG-NAG-BMA.1, NAG-NAG-BMA.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.32, A:S.128 Water bridges: A:N.44

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Banerjee, S. et al., Structure of a heterogeneous, glycosylated, lipid-bound, in vivo-grown protein crystal at atomic resolution from the viviparous cockroach Diploptera punctata. Iucrj (2016)

Release Date

2015-12-02

Peptides

Milk protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Milk protein