SMTL ID : 2fa7.1

Crystal structure of the complex of bovine lactoferrin C-lobe with a pentasaccharide at 2.38 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.38 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: 7 residues within 4Å: Chain A: Y.1, Q.23, S.24, N.27, H.272, Q.273, L.276 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.1

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

NAG-NDG-MAN-BMA-BMA.2: 7 residues within 4Å: Chain A: G.131, L.132, N.135, T.326, A.327, N.330 Ligands: NAG-NAG-NAG-NAG-NDG.4 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:A.327 Hydrogen bonds: A:N.135, A:N.330, A:N.330

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

NAG-NAG-MAN-BMA-BMA-MAN.3: 8 residues within 4Å: Chain A: K.75, S.77, L.93, N.204, D.205, W.208, R.225, Q.244 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.208 Hydrogen bonds: A:S.77

1 x NAG- NAG- NAG- NAG- NDG: 2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-NAG-NAG-NDG.4: 8 residues within 4Å: Chain A: P.88, T.89, L.310, G.311, E.318, G.321, T.322 Ligands: NAG-NDG-MAN-BMA-BMA.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.89, A:L.310

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

SO4.5: 2 residues within 4Å: Chain A: R.229, R.237 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.229, A:R.237

3 x ZN: ZINC ION(Non-covalent)

ZN.6: 2 residues within 4Å: Chain A: G.312, E.318 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.318, A:E.318, H2O.4 ZN.7: 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.6, H2O.6, H2O.10 ZN.8: 4 residues within 4Å: Chain A: Y.1, T.2, R.3, H.265 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:Y.1, A:H.265, H2O.9, H2O.9

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

FE.9: 5 residues within 4Å: Chain A: D.54, Y.92, Y.185, H.254 Ligands: CO3.10 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)

CO3.10: 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.9 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.122

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, N. et al., Crystal structure of the complex of bovine lactoferrin C-lobe with a pentasaccharide at 2.38 A resolution. To be Published

Release Date

2005-12-13

Peptides

Lactotransferrin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactotransferrin

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