SMTL ID : 7equ.1

Crystal structure of the C-lobe of lactoferrin produced by limited proteolysis using pepsin at 2.74A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.74 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, Q.268, H.272, Q.273, L.276 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.2: 8 residues within 4Å: Chain A: R.74, S.77, L.93, N.204, D.205, W.208, E.214, Q.244 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.76 NAG-NAG-BMA.3: 9 residues within 4Å: Chain B: S.76, S.77, L.93, N.204, D.205, W.208, E.214, A.243, Q.244 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.76, B:S.77

2 x NAG- NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG-NAG.4: 3 residues within 4Å: Chain B: N.27, H.272, L.276 No protein-ligand interaction detected (PLIP) NAG-NAG.5: 3 residues within 4Å: Chain A: Q.22, Q.23 Chain B: N.135 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.23

1 x NAG- NAG- BMA: beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose

NAG-NAG-BMA.6: 5 residues within 4Å: Chain A: N.135, E.323, T.326, A.327, N.330 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:E.323 Hydrogen bonds: A:N.330

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

FE.7: 5 residues within 4Å: Chain A: D.54, Y.92, Y.185, H.254 Ligands: BCT.8 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:D.54, A:Y.92, A:Y.185, A:H.254 FE.9: 5 residues within 4Å: Chain B: D.54, Y.92, Y.185, H.254 Ligands: BCT.10 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.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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.122 BCT.10: 10 residues within 4Å: Chain B: D.54, Y.92, T.118, R.122, T.123, A.124, G.125, Y.185, H.254 Ligands: FE.9 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.118, B:R.122, B:A.124, B:G.125

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maurya, A. et al., Crystal structure of the C-lobe of lactoferrin produced by limited proteolysis using pepsin at 2.74A resolution. To Be Published

Release Date

2021-05-19

Peptides

Lactotransferrin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Lactotransferrin

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