SMTL ID : 5cry.1

Structure of iron-saturated C-lobe of bovine lactoferrin at pH 6.8 indicates the softening of iron coordination

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.79 Å

Oligo State

homo-dimer

Ligands

3 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: 7 residues within 4Å: Chain A: Q.23, S.24, N.27, H.272, Q.273, L.276 Chain B: K.333 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 7 residues within 4Å: Chain A: S.77, L.93, N.204, D.205, W.208, E.214, Q.244 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 8 residues within 4Å: Chain B: S.76, S.77, L.93, N.204, D.205, W.208, E.214, Q.244 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.76, B:S.77

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

FE.4: 5 residues within 4Å: Chain A: D.54, Y.92, Y.185, H.254 Ligands: BCT.5 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.54, A:Y.92, A:Y.185, A:H.254 FE.8: 5 residues within 4Å: Chain B: D.54, Y.92, Y.185, H.254 Ligands: BCT.9 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.54, B:Y.92, B:Y.185, B:H.254

2 x BCT: BICARBONATE ION(Non-functional Binders)

BCT.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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.122 BCT.9: 9 residues within 4Å: Chain B: D.54, Y.92, T.118, R.122, T.123, A.124, G.125, Y.185 Ligands: FE.8 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.122

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

NAG.6: 5 residues within 4Å: Chain B: S.24, N.27, H.272, Q.273, L.276 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.273 NAG.7: 2 residues within 4Å: Chain B: N.135, Q.136 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Q.136 Hydrogen bonds: B:N.135

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, A. et al., Structure of iron-saturated C-lobe of bovine lactoferrin at pH 7.0 indicates the softening of iron coordination. To Be Published

Release Date

2015-10-14

Peptides

Lactotransferrin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Lactotransferrin

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