SMTL ID : 4dig.1

Crystal Structure of C-lobe of Bovine lactoferrin Complexed with N-acetylmuramyl l-alanyl d-isoglutamine at 1.8 A Resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

monomer

Ligands

1 x LEU- GLU- ALA- CYS- ALA- PHE: C-terminal peptide from Lactotransferrin(Non-covalent)

LEU-GLU-ALA-CYS-ALA-PHE.1: 8 residues within 4Å: Chain A: D.37, I.40, V.41, L.44, T.60, K.63, C.64, A.329 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:D.37, A:I.40, A:V.41, A:L.44, A:T.60, A:A.329 Hydrogen bonds: A:K.63

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.2: 7 residues within 4Å: Chain A: G.131, L.132, N.135, E.323, T.326, A.327, N.330 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.323, A:E.323, A:N.330 NAG-NAG.3: 8 residues within 4Å: Chain A: K.75, S.76, L.93, N.204, D.205, W.208, E.214, Q.244 No protein-ligand interaction detected (PLIP)

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

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

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

FE.5: 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

2 x ZN: ZINC ION(Non-covalent)

ZN.6: 2 residues within 4Å: Chain A: G.312, E.318 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.318, A:E.318, H2O.4 ZN.7: 2 residues within 4Å: Chain A: H.247 Ligands: DGN.10 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.247, H2O.9

1 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.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.118, A:T.123, A:A.124, A:G.125

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.9: 3 residues within 4Å: Chain A: K.100, R.229, R.237 5 PLIP interactions: 5 interactions with chain A Water bridges: A:R.229, A:R.237, A:R.237 Salt bridges: A:R.229, A:R.237

1 x DGN: D-GLUTAMINE(Non-covalent)

DGN.10: 4 residues within 4Å: Chain A: V.250 Ligands: ZN.7, ALA.11, LAC.12 1 PLIP interactions: 1 interactions with chain A Water bridges: A:V.250

1 x ALA: ALANINE(Non-covalent)

ALA.11: 5 residues within 4Å: Chain A: V.250, E.323 Ligands: DGN.10, LAC.12, NDG.13 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.250, A:V.250

1 x LAC: LACTIC ACID(Non-covalent)

LAC.12: 6 residues within 4Å: Chain A: V.250, A.251, P.252 Ligands: DGN.10, ALA.11, NDG.13 2 PLIP interactions: 1 Ligand-Ligand interactions, 1 interactions with chain A Hydrophobic interactions: A.11, A:V.250

1 x NDG: 2-acetamido-2-deoxy-alpha-D-glucopyranose(Non-covalent)

NDG.13: 10 residues within 4Å: Chain A: T.89, G.91, V.250, A.251, P.252, N.253, E.318, Y.319 Ligands: ALA.11, LAC.12 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.89, A:N.253, A:Y.319, A:Y.319 Water bridges: A:E.318

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shukla, P.K. et al., Crystal Structure of C-lobe of Bovine lactoferrin Complexed with N-acetylmuramyl l-alanyl d-isoglutamine at 1.8 A Resolution. To be Published

Release Date

2012-02-15

Peptides

Lactotransferrin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactotransferrin

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