SMTL ID : 2ays.1

A conserved non-metallic binding site in the C-terminal lobe of lactoferrin: Structure of the complex of C-terminal lobe of bovine lactoferrin with N-acetyl galactosamine at 1.86 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.86 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(Post Translational Modification)

NAG-NAG-BMA.1: 6 residues within 4Å: Chain A: G.131, 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- 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: 9 residues within 4Å: Chain A: K.75, S.77, L.93, N.204, D.205, W.208, E.214, R.225, Q.244 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.77

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

NAG.3: 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

1 x A2G: 2-acetamido-2-deoxy-alpha-D-galactopyranose(Non-covalent)

A2G.4: 4 residues within 4Å: Chain A: T.89, P.252, G.311, Y.319 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.89 Water bridges: A:T.89

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.9 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.7, H2O.9

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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.100 Water bridges: A:R.229 Salt bridges: A:R.229, A:R.237

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, N. et al., A conserved non-metallic binding site in the C-terminal lobe of lactoferrin: Structure of the complex of C-terminal lobe of bovine lactoferrin with N-acetyl galactosamine at 1.86 A 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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