SMTL ID : 2dyx.1

Structure of the complex of lactoferrin C-lobe with melibiose at 2.0 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x NAG- NAG- BMA- MAN- BMA: alpha-D-mannopyranose-(1-4)-[beta-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-BMA.1: 6 residues within 4Å: Chain A: G.131, L.132, N.135, E.323, T.326, N.330 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.323, 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: 7 residues within 4Å: Chain A: S.77, L.93, N.204, D.205, W.208, E.214, Q.244 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.77, A:S.77

1 x BGC- GAL: beta-D-galactopyranose-(1-6)-beta-D-glucopyranose(Non-covalent)

BGC-GAL.4: 9 residues within 4Å: Chain A: T.89, A.251, P.252, E.318, Y.319, L.320, G.321, T.322, E.323 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.89, A:E.90, A:T.322, A:E.323 Water bridges: A:E.318

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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.118, A:R.122, A:A.124, A:G.125

2 x ZN: ZINC ION(Non-covalent)

ZN.7: 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.7 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.6, H2O.6, H2O.11

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

SO4.9: 2 residues within 4Å: Chain A: R.229, R.237 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.237 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 complex of lactoferrin C-lobe with melibiose at 2.0 A resolution. To be Published

Release Date

2006-10-03

Peptides

Lactotransferrin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactotransferrin

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