SMTL ID : 3ib0.1

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 diclofenac

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 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: 7 residues within 4Å: Chain A: Y.1, Q.23, S.24, N.27, H.272, Q.273, L.276 No protein-ligand interaction detected (PLIP)

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: 8 residues within 4Å: Chain A: G.131, L.132, N.135, E.323, T.326, A.327, N.330 Ligands: DIF.6 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: 11 residues within 4Å: Chain A: K.75, S.76, S.77, K.78, H.79, L.93, N.204, D.205, W.208, E.214, Q.244 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:E.214 Hydrogen bonds: A:S.76 Water bridges: A:R.225

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

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

CO3.5: 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.4 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.118, A:R.122

1 x DIF: 2-[2,6-DICHLOROPHENYL)AMINO]BENZENEACETIC ACID(Non-covalent)

DIF.6: 7 residues within 4Å: Chain A: P.252, E.318, Y.319, L.320, G.321, T.322 Ligands: NAG-NAG-MAN-MAN-MAN.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:P.252, A:Y.319, A:Y.319 Hydrogen bonds: A:E.318, A:T.322, A:T.322 Water bridges: A:E.323

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

SO4.7: 3 residues within 4Å: Chain A: K.100, R.229, R.237 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.229, A:R.229, A:R.237 Salt bridges: A:R.229, A:R.237 SO4.8: 4 residues within 4Å: Chain A: Y.1, T.2, R.262, H.265 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.2, A:R.262 Salt bridges: A:H.265

2 x ZN: ZINC ION(Non-covalent)

ZN.9: 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.17 ZN.10: 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.3, H2O.17, H2O.17

1 x EOH: ETHANOL(Non-functional Binders)

EOH.11: 4 residues within 4Å: Chain A: V.134, G.138, S.139, C.140 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.134 Water bridges: A:C.140

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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