SMTL ID : 2alu.1

Detection of new binding site in the C-terminal lobe of lactoferrin:Crystal structure of the complex formed between bovine lactoferrin and a tetrasaccharide at 2.1A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

monomer

Ligands

1 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: G.131, L.132, N.135, T.326, A.327, N.330 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.330 Water bridges: A:T.326, A:T.326

1 x NAG- NAG- BMA- MAN- MAN- MAN: alpha-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-alpha-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-MAN-MAN-MAN.2: 8 residues within 4Å: Chain A: L.93, N.204, D.205, W.208, G.213, E.214, R.225, Q.244 No protein-ligand interaction detected (PLIP)

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

NAG-NDG-NAG-NAG.3: 7 residues within 4Å: Chain A: P.252, P.314, E.318, Y.319, L.320, G.321, E.323 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.323

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

NAG.4: 6 residues within 4Å: Chain A: Q.23, S.24, N.27, H.272, Q.273, L.276 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.276 Hydrogen bonds: A:N.27, A:Q.273

2 x ZN: ZINC ION(Non-covalent)

ZN.5: 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.8 ZN.6: 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.7, H2O.8, H2O.8

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

FE.7: 5 residues within 4Å: Chain A: D.54, Y.92, Y.185, H.254 Ligands: CO3.8 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)

CO3.8: 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.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.118, A:A.124, A:G.125

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

SO4.9: 3 residues within 4Å: Chain A: K.100, R.229, R.237 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.100 Salt bridges: A:R.229, A:R.237

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, N. et al., Detection of new binding site in the C-terminal lobe of lactoferrin:Crystal structure of the complex formed between bovine lactoferrin and a tetrasaccharide at 2.1A resolution. To be Published

Release Date

2005-09-20

Peptides

Lactotransferrin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactotransferrin

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