SMTL ID : 2dvc.1

Structure of the bovine lactoferrin C-lobe complex with sucrose at 3.0 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN- MAN: alpha-D-mannopyranose-(1-4)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA-MAN-MAN.1: 5 residues within 4Å: Chain A: L.132, N.135, T.326, A.327, N.330 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.326, A:N.330

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.2: 6 residues within 4Å: Chain A: Q.23, S.24, N.27, H.272, Q.273, L.276 No protein-ligand interaction detected (PLIP)

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

NAG-NAG-BMA-BMA-MAN-BMA.3: 9 residues within 4Å: Chain A: K.75, S.77, S.80, L.93, N.204, D.205, W.208, R.225, Q.244 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.80 Hydrophobic interactions: A:W.208

1 x GLC- FRU: beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose(Non-covalent)

GLC-FRU.4: 6 residues within 4Å: Chain A: E.317, E.318, Y.319, G.321, T.322, E.323 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.318, A:T.322, A:T.322

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

FE.5: 5 residues within 4Å: Chain A: D.54, Y.92, Y.185, H.254 Ligands: CO3.6 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)

CO3.6: 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.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.118, A:A.124, A:G.125

2 x ZN: ZINC ION(Non-covalent)

ZN.7: 1 residues within 4Å: Chain A: E.318 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.318, A:E.318, H2O.5 ZN.8: 1 residues within 4Å: Chain A: H.247 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.247, H2O.5, H2O.5, H2O.5

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

SO4.9: 2 residues within 4Å: Chain A: R.229, R.237 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.229, A:R.229 Salt bridges: A:R.229, A:R.237

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mir, R. et al., Structure of the bovine lactoferrin C-lobe complex with sucrose at 3.0 A resolution. To be Published

Release Date

2006-08-15

Peptides

Lactotransferrin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactotransferrin

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