SMTL ID : 3ib1.1

Structural basis of the prevention of NSAID-induced damage of the gastrointestinal tract by C-terminal half (C-lobe) of bovine colostrum protein lactoferrin: Binding and structural studies of C-lobe complex with indomethacin

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 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:T.326, A:N.330 Water bridges: A:E.323

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.2: 7 residues within 4Å: Chain A: K.75, N.204, D.205, W.208, E.214, R.225, Q.244 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 2 residues within 4Å: Chain A: R.313, E.318 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.318, A:E.318, H2O.5 ZN.4: 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.5, H2O.5, H2O.6

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

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

SO4.7: 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

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

NAG.8: 5 residues within 4Å: Chain A: 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 IMN: INDOMETHACIN(Non-covalent)

IMN.9: 5 residues within 4Å: Chain A: P.88, T.89, E.90, G.321, T.322 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.322, A:T.322 Water bridges: A:T.322

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mir, R. et al., The structural basis for the prevention of nonsteroidal antiinflammatory drug-induced gastrointestinal tract damage by the C-lobe of bovine colostrum lactoferrin. Biophys.J. (2009)

Release Date

2009-08-11

Peptides

Lactotransferrin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactotransferrin

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