SMTL ID : 7enu.1

Crystal structure of iron-saturated C-terminal half of lactoferrin produced proteolytically using pepsin at 2.32A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.32 Å

Oligo State

homo-dimer

Ligands

3 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: 1 residues within 4Å: Chain A: N.135 No protein-ligand interaction detected (PLIP) NAG-NAG.4: 6 residues within 4Å: Chain B: Q.23, S.24, N.27, H.272, Q.273, L.276 No protein-ligand interaction detected (PLIP) NAG-NAG.6: 3 residues within 4Å: Chain A: Q.22, Q.23 Chain B: N.135 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.22, A:Q.23

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.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)

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

NAG-NAG-BMA-MAN.3: 10 residues within 4Å: Chain B: K.75, S.76, S.77, S.80, 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.80

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

NAG-NAG-BMA-MAN-MAN.5: 10 residues within 4Å: Chain A: R.74, K.75, S.77, H.79, L.93, N.204, D.205, W.208, E.214, Q.244 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.77

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: CO3.8 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: CO3.10 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:D.54, B:Y.92, B:Y.185, B:H.254

2 x CO3: CARBONATE ION(Non-functional Binders)

CO3.8: 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 CO3.10: 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 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.118, B:T.123, B:A.124

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, J. et al., Crystal structure of iron-saturated C-terminal half of lactoferrin produced proteolytically using pepsin at 2.32A 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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