SMTL ID : 3ugw.1

Crystal Structure of C-lobe of Bovine lactoferrin Complexed with Deoxycytidine at 1.87 A Resolution

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.87 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: 7 residues within 4Å: Chain A: D.37, I.40, V.41, T.60, K.63, C.64, K.333 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:D.37, A:I.40, A:V.41, 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: 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: 7 residues within 4Å: Chain A: L.93, N.204, D.205, W.208, E.214, Q.244 Ligands: DCZ.11 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.77, A:S.77 Water bridges: A:R.225

2 x ZN: ZINC ION(Non-covalent)

ZN.4: 2 residues within 4Å: Chain A: G.312, E.318 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:E.318, A:E.318 ZN.5: 2 residues within 4Å: Chain A: H.247, V.250 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.247, H2O.12

1 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

1 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 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.118, A:R.122

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

SO4.8: 3 residues within 4Å: Chain A: K.100, R.229, R.237 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.237 Water bridges: A:K.100, A:R.229, A:R.229 Salt bridges: A:R.229, A:R.237

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

NAG.9: 6 residues within 4Å: Chain A: Q.23, S.24, N.27, H.272, Q.273, L.276 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.276 Hydrogen bonds: A:N.27, A:Q.273 Water bridges: A:T.2, A:T.2

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 6 residues within 4Å: Chain A: E.12, K.15, K.16, Q.19, S.293, L.298 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.12, A:K.16, A:Q.19 Water bridges: A:Q.19

1 x DCZ: 2'-DEOXYCYTIDINE(Non-covalent)

DCZ.11: 7 residues within 4Å: Chain A: R.74, E.90, G.91, Y.92, L.93, Q.244 Ligands: NAG-NAG.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Q.244 Hydrogen bonds: A:R.74, A:G.91, A:L.93 Water bridges: A:Q.244

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 Deoxycytidine at 1.87 A Resolution. To be Published

Release Date

2011-11-16

Peptides

Lactotransferrin: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lactotransferrin

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