SMTL ID : 3k0v.1

Removal of sugars and sugars-like molecules from the solution by C-lobe of lactoferrin: Crystal structure of the complex of C-lobe with beta-D-glucopyranosyl-(1->4)-beta-D-galactopyranosyl-(1->4)-alpha-D-glucopyranose at 1.9 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.91 Å

Oligo State

monomer

Ligands

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.1: 5 residues within 4Å: Chain A: S.24, N.27, H.272, Q.273, L.276 No protein-ligand interaction detected (PLIP)

2 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(Post Translational Modification)

NAG-NAG-MAN.2: 4 residues within 4Å: Chain A: G.131, L.132, N.135, N.330 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.330 NAG-NAG-MAN.3: 8 residues within 4Å: Chain A: K.75, L.93, N.204, D.205, W.208, E.214, A.243, Q.244 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.225 Hydrogen bonds: A:K.75, A:K.75

1 x GLC- GAL- BGC: beta-D-glucopyranose-(1-4)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose

GLC-GAL-BGC.4: 9 residues within 4Å: Chain A: E.90, V.250, A.251, P.252, E.318, Y.319, G.321, T.322, E.323 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.318, A:T.322, A:T.322, A:T.322, A:V.250, A:E.323, A:E.323, A:E.323 Water bridges: A:T.89, A:T.89, A:Y.319, A:Y.319, A:T.89

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 3 residues within 4Å: Chain A: K.100, R.229, R.237 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.229 Salt bridges: A:R.229, A:R.237

2 x ZN: ZINC ION(Non-covalent)

ZN.6: 2 residues within 4Å: Chain A: G.312, E.318 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.318, A:E.318 ZN.7: 1 residues within 4Å: Chain A: H.247 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.247, H2O.4, H2O.15

1 x FE: FE (III) ION(Non-covalent)

FE.8: 5 residues within 4Å: Chain A: D.54, Y.92, Y.185, H.254 Ligands: CO3.9 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.54, A:Y.92, A:Y.185, A:H.254

1 x CO3: CARBONATE ION(Non-functional Binders)

CO3.9: 10 residues within 4Å: Chain A: D.54, Y.92, T.118, R.122, T.123, A.124, G.125, Y.185, H.254 Ligands: FE.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.122

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mir, R. et al., Specific interactions of C-terminal half (C-lobe) of lactoferrin protein with edible sugars: binding and structural studies with implications on diabetes. Int.J.Biol.Macromol. (2010)

Release Date

2009-10-13

Peptides

Lactotransferrin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactotransferrin

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