SMTL ID : 7fdw.1

Crystal structure of pepsin cleaved lactoferrin C-lobe at 2.28 A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.28 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: 9 residues within 4Å: Chain A: K.75, S.76, 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:K.75 NAG-NAG-BMA.2: 6 residues within 4Å: Chain A: Q.23, S.24, N.27, H.272, Q.273, L.276 No protein-ligand interaction detected (PLIP) NAG-NAG-BMA.3: 9 residues within 4Å: Chain B: K.75, 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:K.75, B:K.75, B:S.76

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: CO3.5 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: CO3.9 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.54, B:Y.92, B:Y.185, B:H.254

2 x 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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.122 CO3.9: 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.8 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:T.118, B:T.123, B:A.124, B:G.125

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

NAG.6: 3 residues within 4Å: Chain A: Q.22, Q.23 Chain B: N.135 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:N.135, A:Q.23 NAG.7: 6 residues within 4Å: Chain B: Q.23, S.24, N.27, H.272, Q.273, L.276 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:L.276 Hydrogen bonds: B:N.27, B:H.272, B:Q.273

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, J. et al., A Peptide Bond from the Inter-lobe Segment in the Bilobal Lactoferrin Acts as a Preferred Site for Cleavage for Serine Proteases to Generate the Perfect C-lobe: Structure of the Pepsin Hydrolyzed Lactoferrin C-lobe at 2.28 angstrom Resolution. Protein J. (2021)

Release Date

2021-08-04

Peptides

Lactotransferrin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Lactotransferrin

Related Entries With Identical Sequence