SMTL ID : 2dp8.1

Carbohydrate recognition by lactoferrin: Crystal structure of the complex of C-terminal lobe of bovine lactoferrin with trisaccharide at 2.5 A resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.50 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: 6 residues within 4Å: Chain A: Y.1, S.24, G.25, N.27, H.272, L.276 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.1

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

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

1 x NAG- NAG- MAN- MAN- MAN- MAN: alpha-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-alpha-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-MAN-MAN-MAN.3: 7 residues within 4Å: Chain A: K.75, L.93, N.204, D.205, W.208, E.214, Q.244 No protein-ligand interaction detected (PLIP)

1 x NAG- NAG- NAG: 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.4: 7 residues within 4Å: Chain A: E.90, V.250, P.252, E.318, Y.319, L.320, G.321 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.90, A:E.318, A:Y.319, A:L.320 Water bridges: A:E.323

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: 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.3 ZN.8: 1 residues within 4Å: Chain A: H.247 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.247, H2O.6, H2O.6

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

SO4.9: 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

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, N. et al., Carbohydrate recognition by lactoferrin: Crystal structure of the complex of C-terminal lobe of bovine lactoferrin with trisaccharide at 2.5 A resolution. To be Published

Release Date

2006-05-23

Peptides

Lactotransferrin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactotransferrin

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