SMTL ID : 3vdf.1

Crystal Structure of C-lobe of Bovine lactoferrin Complexed with diaminopimelic acid at 1.46 A Resolution

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.46 Å

Oligo State

monomer

Ligands

1 x LEU- GLU- ALA- CYS- ALA- PHE: C-TERMINAL PEPTIDE OF LACTOTRANSFERRIN(Non-covalent)

LEU-GLU-ALA-CYS-ALA-PHE.1: 7 residues within 4Å: Chain A: D.37, I.40, V.41, L.44, T.60, K.63, C.64 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:D.37, A:I.40, A:V.41, A:L.44, A:T.60 Hydrogen bonds: A:K.63, A:K.63 Water bridges: A:Y.59

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: 8 residues within 4Å: Chain A: G.131, L.132, N.135, E.323, T.326, A.327, N.330 Ligands: API.10 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.323, A:N.330 NAG-NAG.3: 10 residues within 4Å: Chain A: K.75, S.76, S.77, L.93, N.204, D.205, W.208, E.209, E.214, Q.244 1 PLIP interactions: 1 interactions with chain A Water bridges: A:K.75

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 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.276 Hydrogen bonds: A:N.27, 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.15 ZN.7: 2 residues within 4Å: Chain A: H.247 Ligands: API.10 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.247, API.10

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 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.122

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

SO4.9: 3 residues within 4Å: Chain A: K.100, R.229, R.237 6 PLIP interactions: 6 interactions with chain A Water bridges: A:K.100, A:R.229, A:R.229, A:R.237 Salt bridges: A:R.229, A:R.237

1 x API: 2,6-DIAMINOPIMELIC ACID(Non-covalent)

API.10: 10 residues within 4Å: Chain A: I.128, H.247, L.248, A.249, V.250, E.323, Y.324, A.327 Ligands: NAG-NAG.2, ZN.7 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:A.249 Hydrogen bonds: A:V.250, A:V.250 Water bridges: A:H.247 Salt bridges: A:H.247

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 diaminopimelic acid at 1.46 A Resolution. To be Published

Release Date

2012-01-18

Peptides

Lactotransferrin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactotransferrin

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