SMTL ID : 7ev0.1

Crystal structure of pepsin cleaved C-terminal half of lactoferrin at 2.7A resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

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.1: 5 residues within 4Å: Chain A: Q.22, Q.23 Chain B: N.135, Q.136, N.330 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.23 NAG-NAG.4: 5 residues within 4Å: Chain B: T.2, S.24, N.27, H.265, H.272 No protein-ligand interaction detected (PLIP)

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: 5 residues within 4Å: Chain A: Q.23, S.24, N.27, H.272, Q.273 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.272

2 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: 8 residues within 4Å: Chain B: K.75, S.76, S.80, L.93, N.204, D.205, W.208, E.214 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.76, B:S.80, B:S.80 NAG-NAG-BMA-MAN.5: 12 residues within 4Å: Chain A: R.74, K.75, S.76, S.77, H.79, S.80, L.93, N.204, D.205, W.208, E.209, Q.244 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.76, A:S.80

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

FE.6: 5 residues within 4Å: Chain A: D.54, Y.92, Y.185, H.254 Ligands: CO3.7 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)

CO3.7: 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.6 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 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.122

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

NAG.8: 5 residues within 4Å: Chain A: G.131, L.132, N.135, A.327, N.330 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.132, A:A.327 Hydrogen bonds: A:N.330

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Singh, J. et al., Crystal structure of pepsin cleaved C-terminal half of lactoferrin at 2.7A resolution. To Be Published

Release Date

2021-06-02

Peptides

Lactotransferrin: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
P

Lactotransferrin

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